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Warm/Hot Starting Issue (air related?) - ‘06 Speedster 200

Boat - 2006 Sea Doo Speedster 200 Wake.

I’ve been fighting this issue for too long and I’m frustrated and out of ideas. What I’m experiencing is the Port side motor not firing up after the engine is warm. Starboard fires up with no issues whatsoever. Initially, it was limited to only when the boat was on the water. Now, it won’t start on the trailer after it’s warm. It cranks and sometimes stumbles as if it’s about the start, but doesn’t end up turning over. My temporary fix is when it’s stumbling to start (so I can get some use out of the boat for the year) is to throw it into gear really fast and hit the accelerator. This takes about 5-7 tries, but it eventually gets it going. This prompted me to have someone else start the boat while I open the throttle body by hand and it starts right away. So, I’m thinking an air issue.

What I’ve done to attempt to fix it:

I swapped the following from my starboard motor with no change to either motor:
Idle bypass valve / idle air control valve
Throttle position sensor
Throttle body
MAP Sensor


Completed:
Compression Test - 145, 142, 134 (better than starboard compression at 143, 140, 134)
Fuel Pressure Test - 46-48 psi. (on a new aftermarket fuel pump)

Replaced:
Fuel pump
Fuel filter
Fuel Pressure Regulator
Rectifier
Spark Plugs (gapped)
Coil Packs
Spark Plug Tubes
Stator
Crankshaft Position Sensor
Camshaft Position Sensor
Rebuilt Injectors and swapped injectors with starboard injectors
Starter
Starter Relay
Added 4gauge ground wire directly to battery
Gutted TOPS Valve

I plan on doing a leak down test and swapping the engine harnesses, but after that, I’m fresh out of ideas. I feel like I’m onto something with the throttle body/air intake, but I really don’t know for sure. I can’t take it anywhere to be fixed because no Sea Doo dealerships will touch boats in my area, so it is on me to resolve it. So, any help someone can offer is greatly appreciated.
 
I also attempted to adjust the throttle cable this morning, but when I reached a point where the engine started, the idle was around 4,000+ rpm.
 
Thanks. No holes/leaks in the J-pipe.Forgot to mention that this was the first thing I looked at when the issue began. The engine has this starting issue on land as well after warming up, so I’m not sure water is part of the equation.
 
I had the same problem with mine (Speedster 150) after engine rebuild and upgraded SC (~320hp), with larger ingectors, the ECU was also remapped and intercooler was upgraded to the external type. The boat was running (starting) fine first 10hrs or so, then the issue began after it warmed up, it was a gradual decline to a point where i had to open the engine bay and twist the throttle manualy while it cranks (fired up righ away). The issue was, the water was getting into the cylinders via the intercooler cooling housing, mechanic pulled out the plugs and all were rusty around rods. Replaced that faulty IC along with remapping the ECU to run a little less "Rich" , this seemed to fix the issue but temporarily. After about 6 hours on water the issue was back but not that bad, the boat would start after 2-4th try. It is now being serviced and they are looking at the ECU maps, apparently the ECU can slightly adjust its settings if you run the boat hard (rapid UP/ DOWN on throttle, full speed for a prolonged time, hard accelleration etc.)
I'll update on this next week when i get it back.
Meanwhile, I'd suggest to check the ECU, if mapping is out of the ordinary... the plugs would be good idea to inspect also but obviously they will take time to accumulate rust which will give the indication of water in cylinders.
 
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