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2004 seadoo challenger1800(Merc sportjet) no start

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Merc Seadoo

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Hello All!

I wanted to start off by saying I'm sorry I am new to this forum and if my issues have already been solved or discussed then please Moderators feel free to link me to the correct one.

I own a 2004 seadoo challenger 1800 and I recently had to have it rebuilt as it blew up on the previous owners mechanic while they were testing it for the season. Now I have rebuilt a couple of 2.5 merc engines especially sportjets so Im pretty familiar with these. I am having a condition where Im getting a low audible continuous beep while I try to start the engine. Now I have confirmed through the build that there is in fact compression equal to all cylinder and have also confirmed fuel pressure and spark. So I go to crank the engine and I hear this continuous beeeeeeeeeeeeep while cranking and nothing. I checked intake with a borascope while someone was cranking and I dont see anything spraying to the reeds. Im wondering if the reason why the engine blew up is because of some sort of sensor went bad while the engine was winding up in RPM and then just cut fuel causing detonation but thats just what Im speculating. I dont want to go and replace sensors or even the ecm without knowing for a fact that its the issue. Im wondering what sensors are detrimental to the engine starting and do not allow the engine to start at all(hard fault). Any suggestions or things to try would be appreciated thank you!
 
Hello All!

I wanted to start off by saying I'm sorry I am new to this forum and if my issues have already been solved or discussed then please Moderators feel free to link me to the correct one.

I own a 2004 seadoo challenger 1800 and I recently had to have it rebuilt as it blew up on the previous owners mechanic while they were testing it for the season. Now I have rebuilt a couple of 2.5 merc engines especially sportjets so Im pretty familiar with these. I am having a condition where Im getting a low audible continuous beep while I try to start the engine. Now I have confirmed through the build that there is in fact compression equal to all cylinder and have also confirmed fuel pressure and spark. So I go to crank the engine and I hear this continuous beeeeeeeeeeeeep while cranking and nothing. I checked intake with a borascope while someone was cranking and I dont see anything spraying to the reeds. Im wondering if the reason why the engine blew up is because of some sort of sensor went bad while the engine was winding up in RPM and then just cut fuel causing detonation but thats just what Im speculating. I dont want to go and replace sensors or even the ecm without knowing for a fact that its the issue. Im wondering what sensors are detrimental to the engine starting and do not allow the engine to start at all(hard fault). Any suggestions or things to try would be appreciated thank you!

Can you define “blew up”?
Open the drain screw on the side of the vst. Fuel should flow as long as the key is on. While you are there, do you feel the pump running inside? The pump is on a timer in the ECM, unless the engine is running.
Not sure about your beep. Should be 1sec beep when you turn key to run. Try pulling the blue wire of the bottom of the large gas filter.
 
Can you define “blew up”?
Open the drain screw on the side of the vst. Fuel should flow as long as the key is on. While you are there, do you feel the pump running inside? The pump is on a timer in the ECM, unless the engine is running.
Not sure about your beep. Should be 1sec beep when you turn key to run. Try pulling the blue wire of the bottom of the large gas filter.
Hey and thanks for assisting me. Blew up as in catastrophic failure lean condition or lack of oil caused a rod to go through the block. Im pretty sure the Vst Is filled with fuel because Im getting fuel pressure at the schrader valve up top. I cant quite remember correctly because its been some time but I'm almost positive I hear the pump whining at first key on. Also which blue wire do you mention under the gas filter? Is it a light or dark blue?
 
Ok so after multiple attempts of cranking it and playing around with all the sensors making sure they are not fried or corroded I started to get some firing(hiccup) within the engine so I kept at it and finally managed to get her fired up. When it was cranking I removed the intake manifold Temp sensor and it seemed to help it get firing on all 6 cylinder. The only issues I am having now which is why I think the old engine self destructed is A ) if I leave it long enough on idle low RPM Ill hear a change in RPM like shudder or spike up briefly and it will start to misfire / bog down into a stall followed by a blueish heavy fuel smell smoke. I did notice after a couple of test runs that one bank of cylinders felt much hotter than the others but maybe not related and if I throttle it and rev her up she clears up and from what it sounds like running good on all cylinders . Also, I noticed that the alternator is getting somewhat hotter than the block or way quicker than the block after just firing it up maybe the alternator is causing bad drops of voltage and in return is making the engine fuel pump or FUel delivery system fail and spark drop or misfire? So I believe I'm having multiple issue that are all resulting in this behavior. Can you tell me perhaps if I have any of the 3 bad Temp sensors what it would be the effects if any? And if you know of these dam alternators having intermittent issues?
 
Ok so after multiple attempts of cranking it and playing around with all the sensors making sure they are not fried or corroded I started to get some firing(hiccup) within the engine so I kept at it and finally managed to get her fired up. When it was cranking I removed the intake manifold Temp sensor and it seemed to help it get firing on all 6 cylinder. The only issues I am having now which is why I think the old engine self destructed is A ) if I leave it long enough on idle low RPM Ill hear a change in RPM like shudder or spike up briefly and it will start to misfire / bog down into a stall followed by a blueish heavy fuel smell smoke. I did notice after a couple of test runs that one bank of cylinders felt much hotter than the others but maybe not related and if I throttle it and rev her up she clears up and from what it sounds like running good on all cylinders . Also, I noticed that the alternator is getting somewhat hotter than the block or way quicker than the block after just firing it up maybe the alternator is causing bad drops of voltage and in return is making the engine fuel pump or FUel delivery system fail and spark drop or misfire? So I believe I'm having multiple issue that are all resulting in this behavior. Can you tell me perhaps if I have any of the 3 bad Temp sensors what it would be the effects if any? And if you know of these dam alternators having intermittent issues?
Alternator is like a car. Put a voltmeter on the output to check. That should show any “drops”. Check all your ground wires. There are several. No green connections allowed.
 
Alternator is like a car. Put a voltmeter on the output to check. That should show any “drops”. Check all your ground wires. There are several. No green connections allowed.
Ok, so maybe I'm being a little over cautious but its not as simple as that. I have checked the output from the alternator and it usually is sitting at around 14.2V sometimes dropping to about 13.8-9. I have narrowed it down to 2 things. Either the alternator somehow having a drop in volts is making all the electronic components go crazy resulting in a irregular Injection pulse from the ecu and causing the each bank of cylinders to misfire ultimately dying down and stalling. Or, I believe its either one of the temp sensors on each bank of the cylinders. I did notice that the engine will start up and run perfect when I swap one side of the wiring harness for the temp sensors to either port or star side but when I swap vice versa it will start up and immediately start chocking up and eventually dying with bunch of smoke(unburnt fuel) occasionally causing mean loud backfires. Excuse my ignorance but I am not sure which bank the yellow sleeved wire harness clip goes into? Right now I have the yellow sleeved clip for the Temp sensor connected to the Port side of the engine Starboard side in order to get it all cleared up and running all cylinders without chocking up and able to move it into drive to rev it up but then I do notice the Startboard side of the engine gets significantly hotter than the Port side. Not sure if this makes sense since I'm dumping all the scenarios at once but hopefully you get what I'm experiencing.
 
Ok, so maybe I'm being a little over cautious but its not as simple as that. I have checked the output from the alternator and it usually is sitting at around 14.2V sometimes dropping to about 13.8-9. I have narrowed it down to 2 things. Either the alternator somehow having a drop in volts is making all the electronic components go crazy resulting in a irregular Injection pulse from the ecu and causing the each bank of cylinders to misfire ultimately dying down and stalling. Or, I believe its either one of the temp sensors on each bank of the cylinders. I did notice that the engine will start up and run perfect when I swap one side of the wiring harness for the temp sensors to either port or star side but when I swap vice versa it will start up and immediately start chocking up and eventually dying with bunch of smoke(unburnt fuel) occasionally causing mean loud backfires. Excuse my ignorance but I am not sure which bank the yellow sleeved wire harness clip goes into? Right now I have the yellow sleeved clip for the Temp sensor connected to the Port side of the engine Starboard side in order to get it all cleared up and running all cylinders without chocking up and able to move it into drive to rev it up but then I do notice the Startboard side of the engine gets significantly hotter than the Port side. Not sure if this makes sense since I'm dumping all the scenarios at once but hopefully you get what I'm experiencing.
If you don’t mind getting shocked by 40,000 volts, you could pull the spark plug wires off each plug of the cold side. Really? There is a tool for that.
Make sure those plugs are getting spark. Are all your spark plugs wet with fuel?

Alternator output will vary. As the battery charge level goes up, the alt. voltage goes down. Merc electronics are usually stable down to 10volts.

Have you tested the temp sensors according to service book? Hot water and ohm meter.

Starting to sound like you have one or more leaking injectors.

Since rebuild, has the ignition timing been checked?
 
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If you don’t mind getting shocked by 40,000 volts, you could pull the spark plug wires off each plug of the cold side. Really? There is a tool for that.
Make sure those plugs are getting spark. Are all your spark plugs wet with fuel?

Alternator output will vary. As the battery charge level goes up, the alt. voltage goes down. Merc electronics are usually stable down to 10volts.

Have you tested the temp sensors according to service book? Hot water and ohm meter.

Starting to sound like you have one or more leaking injectors.

Since rebuild, has the ignition timing been checked?
Hey Tim75,

Sorry it's been quite some time since I've posted. Ive been testing and troubleshooting the boat whenever I have some free time and wanted to bring some good news but I ended up with bad news again. To answer your questions and suggestions,

last time I had the plugs out and checked them firing visually it didn't look like any had a weak spark or didn't fire at all but could have been intermittent so I dont know.

As for the temp sensor I have not tested any of them with ohms and hot water but plan on it even though I'm pretty sure all 3 temps sensors are not the culprit ai would like to confirm once again. I did even up buying 2x used but good temp sensors so I could have a spare to swap just incase though.

The ignition timing has been checked with a strobe and seems to fire correctly since the engine does sometimes run and also have visually checked all the spark plugs firing. What other way is there to ignition time this engine since it's on a crank position sensor and a keyed flywheel to the crankshaft?

This brings me to a segue question which is kind of bizarre to me and hopefully you can answer. Does it matter which of the two plugs for the head temp sensors wiring harness you use on the starboard or Port side of the heads? One has a Yellow sleeve on it and they are both keyed the same. Interestingly enough when I got some life out of the engine or when it finally cleared up and stopped flooding or misfiring I had unplugged the one of the temp sensors on the starboard and the yellowed sleeved temp wiring harness plugged into Port side of the head with the intake manifold temp sensor unplugged also. I would like to know if you could help me understand how these three sensors communicated with the ecm to add or lower the fuel being injected.


Sorry I'm all over the place, but back to the "sounds like you have one or more leaking injectors" comment. You might be right, but what makes you draw up a conclusion like that?

Going back to the alternator which I'm almost positive is over charging or dropping volts at times, here is why I saw its the alternator and I will tie it all together at the end. While troubleshooting in the very beginning and crank the engine when I thought the injectors weren't getting fuel, I did touch the alternator physically and while the heads were cool to the touch because of constant running water the alternator was almost burning. At one point, I did end up putting the volt meter to the battery and as soon as the engine started to misfire or hiccup while running I noticed the battery voltage drop to 6v and back up again sporadically up and down. Now there could be an issue with the alternator if the engine is running but misfiring at a low Rpm which Could draw more power than the alternator can output because it's spinning too slow, but at the time the engine was staying alive so it had to have been at least 900-1100 Rpms.

UPDATE!!: Here is where this situation takes a turn which I thought I had fixed it but then went right back to square one.

This past weekend I ended up swapping the starboard side temp sensor with the one I had purchased and was playing around with the engine with cranking it trying to start it and clearing up some of the flooding. The engine would start misfire or skip then start up run for a bit then when it felt like it just randomly start to misfire and then die again. I'd like to note that when it started multiple times it would run but with excessive smoke coming out of the exhaust and also would like to add that on top of the oil injection I added 1/2 a gallon of oil premix to the full tank of 93 octane I just filled up. I ended up playing with it all day until I got it to idle perfectly and it literally allowed me to put it in F and Rev it pretty high clearing out the smoke. At this power I thought I had fixed it so I drove to the nearest boat ramp and dropped it off in the water to take her for a spin. The results were marvelous. The engine started right up in the water and I was checking everything to make sure it got the proper cooling and such from the "pee-hole" which checked out. I proceeded to take it for a 20 minute ride at different bands of the Rpm without sputtering or misfiring still with some excessive smoke at the low rpms. I did a couple of rippers and the engine was very responsive and would dig into the water and pickup on plane very fast which was a plus. Here is where thing turned ugly. On the way back it was getting dark so I ended up turning on the courtesy lights and the boat navigation lights because it was starting to get dark. As I was putting along at a low rpm, the smell of fuel/oil burnt would start to accumulate along with the smoke coming from the exhaust in the water and then came the misfiring at about half throttle. Three things I noticed on my way back, I would get 4 beeps every 2 minutes or so which didn't effect the way the engine was running when running good and when it started to misfire, I noticed all the lights would flicker as I would try to throttle it in hopes to clear out the flooding or what I thought it was flooding at a low rpm. Everytime I would try to go past quarter Throttle she wouldn't like it and it would start shuttering and misfiring bad along with a very loud continues Beep until I would end up just bringing down the throttle to probably 10% for it to go away. I I'm so sorry for the lengthy story but this boat has taken me on a voyage and I've about had it. Hopefully someone can shed some light, any suggestions would be greatly appreciated.


I have a video of her running outside right before I prepped her to go in the water and also a video in the water doing a stand still full throttle pull if your interested to hear how she sounds.
 
Hey Tim75,

Sorry it's been quite some time since I've posted. Ive been testing and troubleshooting the boat whenever I have some free time and wanted to bring some good news but I ended up with bad news again. To answer your questions and suggestions,

last time I had the plugs out and checked them firing visually it didn't look like any had a weak spark or didn't fire at all but could have been intermittent so I dont know.

As for the temp sensor I have not tested any of them with ohms and hot water but plan on it even though I'm pretty sure all 3 temps sensors are not the culprit ai would like to confirm once again. I did even up buying 2x used but good temp sensors so I could have a spare to swap just incase though.

The ignition timing has been checked with a strobe and seems to fire correctly since the engine does sometimes run and also have visually checked all the spark plugs firing. What other way is there to ignition time this engine since it's on a crank position sensor and a keyed flywheel to the crankshaft?

This brings me to a segue question which is kind of bizarre to me and hopefully you can answer. Does it matter which of the two plugs for the head temp sensors wiring harness you use on the starboard or Port side of the heads? One has a Yellow sleeve on it and they are both keyed the same. Interestingly enough when I got some life out of the engine or when it finally cleared up and stopped flooding or misfiring I had unplugged the one of the temp sensors on the starboard and the yellowed sleeved temp wiring harness plugged into Port side of the head with the intake manifold temp sensor unplugged also. I would like to know if you could help me understand how these three sensors communicated with the ecm to add or lower the fuel being injected.


Sorry I'm all over the place, but back to the "sounds like you have one or more leaking injectors" comment. You might be right, but what makes you draw up a conclusion like that?

Going back to the alternator which I'm almost positive is over charging or dropping volts at times, here is why I saw its the alternator and I will tie it all together at the end. While troubleshooting in the very beginning and crank the engine when I thought the injectors weren't getting fuel, I did touch the alternator physically and while the heads were cool to the touch because of constant running water the alternator was almost burning. At one point, I did end up putting the volt meter to the battery and as soon as the engine started to misfire or hiccup while running I noticed the battery voltage drop to 6v and back up again sporadically up and down. Now there could be an issue with the alternator if the engine is running but misfiring at a low Rpm which Could draw more power than the alternator can output because it's spinning too slow, but at the time the engine was staying alive so it had to have been at least 900-1100 Rpms.

UPDATE!!: Here is where this situation takes a turn which I thought I had fixed it but then went right back to square one.

This past weekend I ended up swapping the starboard side temp sensor with the one I had purchased and was playing around with the engine with cranking it trying to start it and clearing up some of the flooding. The engine would start misfire or skip then start up run for a bit then when it felt like it just randomly start to misfire and then die again. I'd like to note that when it started multiple times it would run but with excessive smoke coming out of the exhaust and also would like to add that on top of the oil injection I added 1/2 a gallon of oil premix to the full tank of 93 octane I just filled up. I ended up playing with it all day until I got it to idle perfectly and it literally allowed me to put it in F and Rev it pretty high clearing out the smoke. At this power I thought I had fixed it so I drove to the nearest boat ramp and dropped it off in the water to take her for a spin. The results were marvelous. The engine started right up in the water and I was checking everything to make sure it got the proper cooling and such from the "pee-hole" which checked out. I proceeded to take it for a 20 minute ride at different bands of the Rpm without sputtering or misfiring still with some excessive smoke at the low rpms. I did a couple of rippers and the engine was very responsive and would dig into the water and pickup on plane very fast which was a plus. Here is where thing turned ugly. On the way back it was getting dark so I ended up turning on the courtesy lights and the boat navigation lights because it was starting to get dark. As I was putting along at a low rpm, the smell of fuel/oil burnt would start to accumulate along with the smoke coming from the exhaust in the water and then came the misfiring at about half throttle. Three things I noticed on my way back, I would get 4 beeps every 2 minutes or so which didn't effect the way the engine was running when running good and when it started to misfire, I noticed all the lights would flicker as I would try to throttle it in hopes to clear out the flooding or what I thought it was flooding at a low rpm. Everytime I would try to go past quarter Throttle she wouldn't like it and it would start shuttering and misfiring bad along with a very loud continues Beep until I would end up just bringing down the throttle to probably 10% for it to go away. I I'm so sorry for the lengthy story but this boat has taken me on a voyage and I've about had it. Hopefully someone can shed some light, any suggestions would be greatly appreciated.


I have a video of her running outside right before I prepped her to go in the water and also a video in the water doing a stand still full throttle pull if your interested to hear how she sounds.

Sounds like you have one or more leaking injectors:
cranking it trying to start it and clearing up some of the flooding.
Rev it pretty high clearing out the smoke.
Your words. Sounds like leaking injectors. "Rev it pretty high" with no load can grenade your engine.

Is your alternator belt driven? Hot? Are you absolutely certain it is wired correctly? A bad battery (won't take a charge) can make alternator run hot.

I am not real familiar with your year engine. What kind of throttle position sensor do you have? It could be telling the ECM that throttle is WOT, but at 10%. ECM would tell injectors to open as if WOT, causing flooding.

93 octane? Waste of money. Compression in a 2 stroke is not high enough to need 93 octane.
 
Sounds like you have one or more leaking injectors:

Your words. Sounds like leaking injectors. "Rev it pretty high" with no load can grenade your engine.

Is your alternator belt driven? Hot? Are you absolutely certain it is wired correctly? A bad battery (won't take a charge) can make alternator run hot.

I am not real familiar with your year engine. What kind of throttle position sensor do you have? It could be telling the ECM that throttle is WOT, but at 10%. ECM would tell injectors to open as if WOT, causing flooding.

93 octane? Waste of money. Compression in a 2
 
I'm not sure if I mentioned it before but the boat has about 130 hours on it in total essentially brand new looking. The engine was rebuilt due to it blowing up from the previous owners. I also wanted to note that the Rpm guage and Speedo gauge do not work, possibly when the old engine blew up, the alternator shorted something?
Either way, How would the injectors become leaky when they are almost brand new and also ran in the water for about 40 minutes with full power no issues no misfire after u got it started the first time? The alternator is belt driven and I did notice one or the times that it started on the hose before I put it in the water that it was getting hotter than the block which only ran for a mere 40 seconds before it sputtered to a stall. Maybe the range of events is not clear but I have a video of it running perfectly and have not moved any wires around besides just confirming today that all the Temp sensors even in the intake manifold seem to ohm out the same so I ruled those out. One thing I also remember is that when putting the reeds in I made sure that they were all sealed tight and no light came through from the pedals. I'm not sure if that relative to the issue but it's worth mentioning all the things I wasn't sure of. Battery is brand new and cranks from for minutes without loosing much power so that out or the question. I have checked and cleaned all fuses and the plugs. As for wiring the engine back together I'm not 100% sure but it ran on the current setup in the water with no issues so why would it have an issue now? Today I fooled around with it and cranked it a couple of times along with taking out the top sparks on each bank so I can remove the temp sensors to make sure they were good. After I put everything back together I cranked it around 12 times about 25 seconds each interval. The engine sounds like it's firing inside and even almost fell into a starting rythym like it was firing and speeding up the rpm to start like the first time I got it started but then would fall back under starter rpm with the shuddering like it was firing internally. One thing that I have noticed is that after repeatedly trying to start it, I occasionally get this gnarly backfire which should like someone let off a bomb. I also forgot to mention that I also put together another engine on a seadoo 2000 challenger 2000 yr with the Statored electrical system and it still runs like a top. I am going to attach pictures of my engines wiring and also the type of TPS I have just incase you catch something.
 
I forgot to mention that when it was running good in the water I would get a 4 beeps it seemed like every 2 minutes or so but didn't effect anything. I believed it was the water in the filter so I ended up removing the water separator and draining it. The fuel in there looked like it was mixed nice blue tint with oil. At this point the only thing I haven't checked with a volt meter is the TPS, injector pulse and I need to confirm spark again from all cylinders. Also there is a light blue wire that is somewhat a ground which Ys tight into one single white wire pictured not sure if thats supposed to ground somewhere in the harness. I believe it was dangling before the engine was rebuilt and it ran fine without it when it ran. Either way pictures are attached please let me know if you see anything out of order. Also maybe it's worth mentioning I only got life out of this engine the first time while unplugging one of the Temp sensors on the head I believe the port side and also the intake manifold Temp sensor.
 

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