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2005 Sea Doo Sportster problem

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Beaston59

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I've been running into a lot of problems with my 05 sea doo sportster. I bought it with a bad motor and knew I had to replace it. I have now replaced it. It started right up but was running really rough and a check engine light was on. Put a computer to it and it was a fuel injector problem in cylinder 3, so I replaced that but it was still running rough and cylinder 3 was not running because it was getting too much gas. Anyway, we solved the problem by buying a new computer. By this time, I thought I had everything figured out. Took it out on the water and ran perfect.... Only for about 2 minutes. It would then loose all power and act like it was in limp mode. But if I gave it anymore throttle than just idle, I would hear a pop. Like its backfiring!
I have no idea what would cause this. There is no sensor going off, no check engine light, nothing! It actually does this everytime I take it out. It's like it overheats in about 2 minutes and then I'm done until it cools down again. Does anybody know what could possibly be going wrong? I've had way too many problems with this boat and I haven't had any fun. All I'm trying to do is get this thing going!!
 
Additional info: I just had the boat out again and didn't run it as hard. I just took the boat up on plane was running about 15 mph and it still has the same problem 2 minutes later! Super frustrated with this whole thing.
 
was it the correct ecu for the engine? make sure the engine # match's the ecu. the engines changed somewhere around 2006.

check/replace plugs, injector wiring damaged or engine ground. also check injector wiring reversed
 
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Yes it is the correct ecu for the boat. There's no damaged wiring and everything is correct! I have no idea what could be causing it. Could there be a hose that is plugged so it's not getting enough water and its overheating really fast?
 
yes it could be but you said no temp light or beep and back firing. you need dealer or candoo to see any occurred faults.
also check cps, (cam position sensor) i believe this is like the temp sensor, will fault but will not leave the fault as active when the dess is removed.
 
Have pretty much tried all options on the boat except for replacing all sensors. It's kind of a guessing game right now. The exhaust is getting the correct water flow and no blocked hoses. When it goes into it's "pissed off mode" (that's what I've been calling it lately), there is no light that shows on the dash.
The boat runs amazing for about 1 minute, then all of a sudden just wants to quit. Doesn't shut down becuz I let completely up on the throttle and I'm able to get it back to the dock by just putting it in gear. When it goes into the pissed off mode, you can just feel the engine start running rough. And then if any throttle is given it backfires and wants to die completely.
 
Hi...did you ever figure this out?? My boat might be having something similar...thanks
 
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