Overheat alarm and rpm problem

I have a 2004 90 Johnson 2stroke. I was having occasional problems with missing in the motor which felt like something was shorting out and not a fuel problem. The last few episodes it seemed when trash was pulled into lower unit screen a hot alarm would sound. When this would happen the motor would not allow me to get over 2500 rpm without cutting out. It wouldn't kill completely, just like it was skipping.
I am not sure what it is going on but thinking it could be a heat sensor. Now the overheating alarm stays on but the motor still has great water pressure and not overheating. Anyone have any helpful info on this?

Check the telltale water stream temp. with your hand, you should be able to hold it there indefinitely, Place hand on cylinder head for a 6 second count,if it burns your fingers she's to hot, A 20 $ infrared digital temp. gun is another way to check if she's running hot. A bad sensor will give you the reduced rpms called limp home mode the ecu shuts down half the cylinders as a precaution to prevent extensive damage to your engine, test the heat sensor

Model # sounds like it is in S.L.O.W mode