[Frank Ucci]

Throttle/shift linkage? Maybe it got knocked a bit off on the grounding.

 

[Frank Ucci]

On the top left side of the motor there is something called a thermo-sensor, located near the thermostat housing. It has a plug on it which ties it into the engine wiring harness. Check that the plug is free from corrosion and fully engaged. I don't know much about the logic of these engines, but if that thermo-sensor is sending a false signal to the ECU, perhaps the ECU thinks the engine is cold and is raising the idle until it thinks the engine has warmed up sufficiently. If the plug is corroded or if the thermo-sensor is failing, it might account for the intermittent problem that you're having. If it were me, I'd take the boat into my nearest Yamaha dealer and pay an expert tell me what was wrong with it.