4000 watt onana generator. Shuts down after a couple of hours. Won't start back for about 30 minutes. The generator has a code that flashes to tell you the problem but don't know what the 3 flashes mean. Seems to me it's getting hot and shutting down

check the current draw from the machine
being a 4000 watt machine if you are drawing 4000 watts it is overloaded as that is the surge power available not constant power which is around 3500 watts
that would account for the requirement of fans to keep it cool
even if It is not 4000 watt what ever capacity it is it is running in an overload situation

Coils do develop thermal issues sometimes - replacing it is a good place to start.

You have a carburetor problem. Stuck float or clogged filter. Gas cannot get into the carb as fast as it is used. Letting it sit for a few minutes will allow the bowl to fill.

Here is support product lookup. Requires more specific numbers about your gp6500.

Shuts down automatically from oil shortage.

Above 40°F, use SAE 30. Below 40°F and down to 10°F, use 10W-30. Below 10°F, use synthetic 5W-30. Oil should be changed after the first 8 hours of operation and every 200 hours of run time thereafter.

sounds like your coil is done

First thing to monitor is the fuel solenoid power. See if it is the thing that goess away to cause shutdown.

Tracing this back there is only a few things that control this: The battery, the low oil shutdown switch, and the run switch, and associated wiring.

If I were to ventture a guess, I would put money on the low oil shutdown switch.

If it runs really rough before shutting down it is most likely a spark plug.

The engine throttle control is out of adjustment. It needs to be set based on the generator frequency
(60 Hz).

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First locate the oil pressure switch and see if you can bypass it,then see if it runs. If not check the fuel filter and fuel pump,make sure solonoid for fuel pump is kicking on.

does it have original oil in it? if so they use a lighter weight oil than recommended for engine break in. change your oil and filter and see if that doesnt solve it.could be thinning out loosing pressure when hot. i have seen this beofore.. :)