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99 GTX RFI -- Limps in the water, runs great out of water

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I have a 1999 Seadoo GTX RFI - 787 Fuel Injected 2-stroke engine. It has been stuck in limp home mode so I went and got the regulator/rectifier replaced. It worked for 30 minutes and started limping again. Now I noticed that it runs fine outside of the water, but limits to 3500 rpm as soon as it sits back in the water. Is this a RAVE issue, or perhaps a temperature issue? Any suggestions would be appreciated.
 
I'm not sure what the compression is yet, I haven't gotten it checked. I was hoping there might be something easier to play around with before I take it in for that. Hypothetically, if my compression is unbalanced will that automatically lead to a rebuild? How much should something like that cost?
 
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