I am pretty sure it is an 60F. 99/00 2 stroke 60 horse with oil injection. (might be a C60, I will have to get a picture tonight of the serial tag. Okay, not mine but it is one of these > Yamaha 60 2 stroke Madras - YouTube or this 2001 Yamaha 60hp 2 Stroke Outboard Motor - YouTube)
I tore the head apart last night and took off the exhaust side water jacket to see if there was anything stuck in there. All was clear. Had a little fine silt built up on stuff but all holes and ports were fully open.
I ran it at the creek last night and it ran really well at first. Started quick, idled off the trailer, idled fine with no buzzer, strong stream from the tell tale. I opened it up and ran a few hundred yards on plane down and back. Pulled back into the bank and let it idle again just sitting there. Took about 15 minutes and the overheat alarm went off. Popped the cowl off and pulled the pink wire from the temp sensor. Buzzer stopped. I think I just isolated it and identified that it is indeed the overheat sensor and not the fuel level sensor. I pulled the fuel level sensor why and the buzzer continued.
So I definitely have an overheat condition. Why is the big mystery. Water is definitely getting into the water jacket, it was wet when I pulled the head. The very top cylinder was not wet though? Either it dried out in the time it I pulled it or it wasn't getting water up there. Still nothing that would visually indicate a blockage. The top cylinder walls looked no different than the bottom two. No scoring or discoloration that would indicate it is not getting oil.
I am going to pull the lower unit off tonight and look at the water pump again.