720 Problems

[ShadeShot]

So I recently finished my 1992 Sea-Doo SP 720 swap. It has dual carbs that I just rebuilt. The biggest problem I have been having is about after 30 minutes of riding (rather hard riding) it starts to hit what seems like a much lower rev limit. It is very consistent, which makes me think its electrical. It happened the first time out, so I rebuilt the carbs. Then it happened the second time out. It also seems that it gets slightly harder to start after it warms up and has worse low end throttle response. Up until the point where it feels like it hits a lower rev limit it feels fine at high speed and is very fast. Any idea what could be going on. I rebuilt the engine with fresh gaskets and compression is supposedly good when I got the engine. I didn't see any evidence of scoring on the pistons or cylinders. Could it be overheating? I recently found out the buzzer isn't working. But I wasn't aware the temp monitor is tied into the MPEM. Checked the spark plugs, they are a nice brown color. Thoughts?