I had a sort of similar problem with my outboard. It went into 'safe mode' after running it for a bit. The shop overhauled the carburetors which did not solve the problem. The shop next changed out the water pump which did not solve the problem. The shop next changed out the thermostat which did not solve the problem. The shop next cleaned out the ports for cooling the engine and the problem was solved.
Regardless, my outboard needed the carburetors cleaned, a new thermostat and a new impeller. It should be good to go for a while. I'll certainly remember to run the gas from the carburetor if I'm not going to use my outboard for any length of time and use ethanol free gasoline.
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