Please help fact check me on cutting off issue

I have an issue with my 1999 Seadoo GTI. The issue is as followed: She starts and run great, then cuts off for a while and starts up again to run great, only to cut off again. The cut off happens about 20 minute in and takes a while to start up again. She just cranks with no combustion after the shut off. it usually starts with a shut off or two and starts right up before not starting up again some time has passed. The ski had a lot of underlining issues that I fixed but the main issue of cutting off and starting up again seems to still be there. The following are things I've done.
1) All vent valves were replaced so it can't be a vent valve, correct?
2) The rotary valve was completely out of spec, .582mm instead of the .300mm it's supposed to be. I had the cover cut to be in spec
3) I didn't do anything with the carbs because when she's running, she feels like a brand new ski, with power all across the power band, did I make a mistake assuming the carb is fine?
4) When I got the ski, the tank was nearly empty, like one gallon of fuel. I filled it up and added water remover (heet). The ski supposedly only sat for a year with the little gas. I've ran 1/2 the tank so far. Can I rule out the fuel?
5) spark plugs changed twice, so i feel I can definitely rule plugs out.
6) Compressions at 130 each cylinder. I pulled the head cover to change the seal. the jug seals didn't get changed because the walls were warped so I just put it back together. She still ran great after. I think some water may be leaking into the lower end, but I pulled the plugs and cranked the engine and no water comes out. Can I move on with engine being an issue like I assume?
7) This ski love taking in water. I can't figure out from where. New carbon seal kit and it's still doing it. I added a bilge pump, but the question is, can water in the hull affect something to cause a short or something. The water is not high enough to be touching anything so I feel I can move on with the water as the culprit. Am I right?

This is what I have right now, I'll update if I remember more.
 
Id definitely recheck your vents to make sure they are going the right way and also for fuel system leaks. Have all the grey tempo lines been replaced?
 
if the water your taking on is warm than you probably have an exhaust leak
I'll check the next time I'm on the water
Id definitely recheck your vents to make sure they are going the right way and also for fuel system leaks. Have all the grey tempo lines been replaced?
I thought it was a fuel system issue so I rebuild the whole thing, minus rebuilding the carb. I double checked and the vents on the right way.
 
I spoke with a top grade car mechanic today, and described how the ski would run great for like 20 min and stop and the next day will start up again like nothing happened. He stated it's likely an electrical issue. He said if it was mechanical the problem would not get fix with time and likely present itself once i tried to start the ski again. I also read on anther pwc forum of a guy that had the same problem, it turned out to be the stator.
 

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Now that I think about it more i agree its most likely electrical, the reason i said fuel is because i was thinkijg maybe there was pressure building up in the tank causing fuel to be cut off or flooded, if you wanted to ruel out a pressure build up issue you could run it without the fuel cap. But I actually think its something electrical now. Does your buzzer work, your engine could be overheating and you dont get the alarm. Also the taking on water, Id run it on the hose to see if you have any cooling leaks.
 
Now that I think about it more i agree its most likely electrical, the reason i said fuel is because i was thinkijg maybe there was pressure building up in the tank causing fuel to be cut off or flooded, if you wanted to ruel out a pressure build up issue you could run it without the fuel cap. But I actually think its something electrical now. Does your buzzer work, your engine could be overheating and you dont get the alarm. Also the taking on water, Id run it on the hose to see if you have any cooling leaks.
Thanks for that info, next time it stops working, I'll remove the cap to see if it starts. That should at least eliminate that issue.

With the ski taking in water, after changing the carbon seal, I connected it to a hose and no water was coming into the ski. I then placed the ski on the water and let it idle and again, no water leak was observed. when I got the ski back to the ramp after it shut off, about 20% of the hull was filled with water. Since then, I've added a bilge pump to make sure I don't sink while trying to figure it out.
 
Was the water warm or cold?
I didn't know to check for something like that. My experience is motorcycle repairs. This is my first jet ski and I'm using my mechanical background to get it running. The seller told me everything was good with the ski when it wasn't. I downloaded the repair manual and didn't worry much since I thought a bike and ski should be about the same, lol I was wrong, there's definitely some differences.

plus, I don't even understand how this thing even ran. It's like the seller never did any maintenance or servicing on this thing. He basically ran it to the ground.
 
Id do tests on the stator, make sure the rectifier is working and also make sure its not overheating.

Do your gauges or buzzer work?
 
Key beeper works buzzer works probably not overheating, when you can look up how to test stator and to test rectifier you can put a volt meter on the battery and it should be around 13v white revving
 
I didn't know to check for something like that. My experience is motorcycle repairs. This is my first jet ski and I'm using my mechanical background to get it running. The seller told me everything was good with the ski when it wasn't. I downloaded the repair manual and didn't worry much since I thought a bike and ski should be about the same, lol I was wrong, there's definitely some differences.

plus, I don't even understand how this thing even ran. It's like the seller never did any maintenance or servicing on this thing. He basically ran it to the ground.
take it out for a ride and when you put it back on the trailer, take the plugs out and feel the water coming out. if its warmer than the water your riding in; chances are pretty good its an exhaust leak
 
I think I solved the problem. I checked the stator this morning. The manual calls for a 0.05-0.6 ohm reading between the two yellow wires. My reading was 0.00. The manual highlights if I get a 0 ohm reading, I have a short circuit. My reading was 0.00 ohm.
 

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So I changed the stator yesterday and went out today to test it. The ski runs like total dog shit now. Any type of gas and it shuts off right away. I'm assuming I screwed up the stator positioning since the new stator didnt have a notch. I centered it as the service manual stated but after looking at the other stator the screw imprint shows that the center was towards the bottom of the screw and not the real center. if anything, I'll use the old stator base to align the notches
 
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If you have warped jugs,, and I did once ,it will run like crap
Also, the water leak appears to be coming from the engine. A stream is coming out from in-between the jug and head, when the ski is in water due to the warped jugs I indicated. I'm going to take the head off again and use a gasket maker product to see if that stops the leak.
 
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Here's my crappy jug walls. I silicone the crap out of it, hopefully it holds. The aftermarket stator I purchased didn't have the mark to line up with the case, so I measured where the line was on the old stator and scraped it onto the new one. My efforts showed that i was not aligned the first time i installed the stator. She's all back together, wish me luck tomorrow for the test drive...
 

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So the mission was a failure... I'm leaning towards POPPS assessment... I put the ski on water and for 40 minutes she ran perfectly. She was hitting speeds she's never seen, 45mph. I checked the engine and the seals were holding and she felt like a beast. I said I'd give her another 20 minutes before calling it a success. At around 20 minutes I noticed I lost 2 mph... ok, I figured let's keep going, must be the wind, maybe it increased and is slowing me down. 10 minutes later, my top speed was 40mph. The next thing I knew, she cut off and wouldn't start like before. I checked the engine and noticed the silicone seal failed and she was seeping water out again from the head cylinder.

I think it's something with the engine like POPPS noted, but im officially done with her, she up for sale for what ever i can get for her. I bought another ski a few weeks back to enjoy the water so Im going to look at this expereince in this manner: "I spent around $2500 on a ski that taught me a whole lot about working on PWC's." I spent $40,000 on a college education so this was a deal.

Here's a pic of my new toy that's keeping me from crying, lol
If you have warped jugs,, and I did once ,it will run like crap
 

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Thats too bad that you couldnt get it going but damn thats a nice seadoo
Yeah I feel that it's too bad also. Wifey said that she didn't believe that I would get it running good because of how old it was and it was treated like garbage before I got it. I told her, everything of production is fixable, you just have to determine if you're willing to pay the cost to repair it. I could probably get it going for another $1200, but I'm not willing to invest almost $4000 on a 25 year old mid level vehicle. If I can sell her for $1000, I think I'll be ok going in a hole for $1500.

Plus i got the 2016 Limited at a seal. The previous owner just wanted it gone asap due to a divorce.
 
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