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2006 Sea Doo Speedster wont stay running

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No vst pressure?
Try swapping the 2 wires on the vst pump. Polarity matters.

When you had the vst apart, did you check that the float valve needle is free to move? They corrode closed from ethanol.

Polarity was correct and the float was free and working. After putting it back together I tested the fuel pressure right at the pump and got 45psi. Leak ckecking the rail and testing the pressure regulator today. If they both test good I’m assuming that the high pressure pump is intermittent, and will replace it and the low pressure pump just to be safe.
 
Yep. I keep a few sizes on hand. It's good for all kinds of projects. And it's relatively cheap.

Thanks. I had some left over from replacing the fuel lines on my chain saw.

Today I finished diagnosing the fuel system by pressure testing the fuel rail and checking the pressure regulator for proper operation. Both checked good. In the end I’ve got a high pressure fuel pump that is working intermittently and a low pressure pump that doesn’t seem to be pumping a lot of volume. Found both pumps and the VST seal on Amazon, they’ll be here Sunday.
 
"A lot of volume" from the low pressure pump is irrelevant. The needle in the VST will stop it.

My bad, I meant to say that it WASN’T pumping much volume.

Got another question. Does the hose connection fitting in the engine compartment that you use to flush out the jet drive also sent water through the cooling system? Reason I ask is that I’d like to run the engine at least at idle for an extended period of time to ensure the fuel system is working good before we put the boat in the water for a final check out.
 
OK... that makes more sense.

Cooling... yes and no. Yes... it should put water up into the engine, and keep it cool. BUT... NO.... because the flush tap is just above the water inlet on the engine. SO... if your garden hose is low volume.... then most of the water will just go out the pump "Inlet", and in turn... the engine will over heat. If you have a large diameter garden hose... and good pressure... it will keep the engine cool. (my house hose is marginal, and will let the engine get hot)
 
OK... that makes more sense.

Cooling... yes and no. Yes... it should put water up into the engine, and keep it cool. BUT... NO.... because the flush tap is just above the water inlet on the engine. SO... if your garden hose is low volume.... then most of the water will just go out the pump "Inlet", and in turn... the engine will over heat. If you have a large diameter garden hose... and good pressure... it will keep the engine cool. (my house hose is marginal, and will let the engine get hot)

Have another question. Replaced the pumps and took the boat out for a shakedown run today. Not trusting it I let it idle at the dock for about 10 minutes before pulling away, and then stuck close in case of an issue.

Engine ran great and had plenty of power until it suddenly shut off and would not restart. Neither fuel pump was running and I suspect the ignition was dead as well. I checked the safety shutoff lanyard, it was fine. Checked two fuses I found in the engine compartment and shook down the wiring harnesses with no change. After we paddled back to the dock, I was messing with the ignition switch and I heard the fuel pumps come on and it fired right up and ran fine. However not wanting to have to paddle back to the dock again, I loaded it up and headed home.

I’m planning to go through the electrical system to see where it lost power. I do know that the emergency shutdown lanyard did not get pulled off. Any ideas for what to check?
 
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