240 EFI Engine RPM Stumble when engine at operating temp (2000 Seadoo Speedster boat)

[2000Speedster]

I have a 2000 Seadoo Speedster with the 240 EFI and near the end of one season the boat was giving me issues. The red light would flash consistently and at certain RPM I would even hear beeps. The boat once warmed up to operating temp it would also stumble when cruising, so I had a mech come by and check it out and he said the ECM plug was loose, so he reconnected it. So now all was once well. However, the boat has now started to stumble/buck/hesitate at cruising speed/RPM. I notice it every time I am towing a wakeboarder, once riding after a few minutes the stumbling starts and I head back to the dock in fear that it's misfiring or running lean (and with no rider it takes a bit more time before the boat starts to hesitate at RPM). Starts fine when hot and runs when the engine is cool no problem until the engine is hot. The stumble/hesitation/buck slows the boat for a second and then RPM returns to normal then repeats after 10 seconds. The longer I drive the more frequent and close together it stumbles.

I've done all the easy checks and tests such as replacing filters, exhaust tubes, gas, tested all fuel pumps, tested various electrical sensors such as the head temp sensor, etc. but haven't found the source of the issue. I've also searched the net and this forum and haven't come across anyone with this issue yet (tons of issues with hot starts but no issues with the boat running when hot).

Any ideas? Could it be thermal expansion of some electrical sensor? More ECM related issues? Could it be the throttle position sensor (but why would it run so well until warmed up)? If it were running too rich I don't think I would experience this "hiccup" in the RPM while driving? Could be something very easy like a loose connection again or maybe something more serious, but I've been through the shop manual (premium user) and feel like I've tried everything...

It does smoke a lot on the first start of the day and it takes some throttle to clear it out and run smoothly at idle, but it has done that since I've owned the boat. I'd love to solve this issue once and for all so I can take riders and tubers again and enjoy the summer because it's been sitting since. Any help or direction on where to look for the fault would be greatly appreciated!

Thanks!

 

[Dr Honda]

It could be a bunch of things. Unfortunately, when it's intermittent... it's hard to find.

On some of these boats... they have a throttle guardian. When they fail... they start to clip the ignition. The unit is there to keep you from reving too high in neutral, or reverse. SO... it's really not needed, and I would simply disconnect it to make sure that's not the problem.

 

[El Toro 33809]

I guess I'm on a spark plug kick today. I don't see where you said you replaced those. Ours had a stumble like you mentioned, and it too was intermittent. Sometimes it would even quit completely, but restart right away. We replaced our plugs and it has run great since.