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engine stalls after 3500 rpm

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sea doo doo

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I have a 97 challenger 1800 with the twin engines. Both engines have been underwater due to sitting up with plug left in boat for a period of time. Got water outta engines, had carbs rebuilt and installed. new fuel lines, new filters, cleaned out baffle and gas tank. Now running on premix instead of injection. Both engines ran good for 5 minutes after carbs were adjusted at local seadoo shop. Engine behind driver runs steady at 3500 rpm after 5 minutes then stalls but starts back up immediately. Actually will stay running if you throttle back before it dies. Brought back to shop to have them check out. They even changed carbs out from one side to the other with no avail. They have advised me that the engine is about to seize up or an electrical problem is happening somewhere. Anyone know my next step before i get upside down in this boat?
 
If it's trying to die above 3500 rpm... then it's a fuel issue. I would be suspect of the fuel select valve since they swapped the carbs, from an engine that was running.

BUT... I do agree with them about the engine going to give up soon. With water sitting in the engine... all the internal parts will start to rust, and pit.
 
boat runs about 50 plus mph for about 5 minutes, then the problem starts in the one engine. Next day, same problem. Noticed that one fuel filter had more gas in it than other. they have rechecked the carbs and added new fuel lines and filters as i said. could it be the safety rev switch? engine sounds and runs much too good to be fixing to lock up. gotta be something simple.
 
If i am seeing fuel run through the filters, would that eliminate the fuel select valve from the problem? and how do you clean it? Engine runs steady at 3500 rpms
 
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