2001 Johnson Overheating Alarm

take a photo of the cylinder head
 
Ok. So I see a beige/brown wire on the right side going from the head into something that says "Spare" (I assume fuse) and a beige/brown wire on the left side near the larger fuse boxes (Siemens). Any idea which to test for the alarm?

Also tried to take a couple shots of the head.
 

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Also, this is from a rearward facing perspective. If you were facing towards the bow, the sides would be reversed.
 
Ok. So I see a beige/brown wire on the right side going from the head into something that says "Spare" (I assume fuse) and a beige/brown wire on the left side near the larger fuse boxes (Siemens). Any idea which to test for the alarm?

The Siemens things are relays. The tan wire from the head comes almost certainly from the thermal switch. I see a piece of rubber hose with clips around it, a common way to protect a connector from getting wet.
Take the clips off, slide the hose over the wire and you will see a single wire Molex connector pair. Pull these two apart and check if the alarm stops. If it does, the switch is defective; if it doesn't the problem is in the wiring to the buzzer.
 
I was trying to determine if its early or late style as it will have a wire going to the ign pack to operate the SLOW function as in if it gets hot it will limit the rpm
Still has the horn though.
The thermostat is behind that cover on the cyl head, I would remove that and have a look.
its a 98 or 99 year engine
 
Pulled the boat for other work and got ready to mess with the wires. Hooked it up to muffler and hose and ran it for ten minutes or so...alarm never went off! Not sure if it was because water was being forced in and kept it cooler, or if disconnecting and re-connecting the beige wire (from the head) reset something.

Will be interesting to see if it does it in the water.
 
Tried the boat in the water. First of all, it's hard to start cold - have to use starting fluid. Ran for a while until it got hot. Buzzer started to partly buzz, but not constant. Revved and unattached beige connection from head, but buzz continued. Stopped and re-started and buzz persisted at idle, but not at higher revs.

Stopped and re-started again and engine went dead. No crank, nothing. Checked battery terminal connections and fuel line. Not even a quick tone when I flipped key to start position. Waited for a few minutes and it cranked. Does this sound like an electrical or overheating problem? Am I doing something wrong? I've recently replaced the plugs, water/fuel separator, lower unit oil and am mixing 50:1 gas:oil.
 
So clearly this was and is no overheating problem but an electrical one.
Normally there is just a single cable running from the engine to the throttle control. Because you also report starting issues I suggest you dismantle the control unit and check for corrosion. It is prone to water intrusion, the ignition lock may be eaten internally if seawater has entered.
 
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