You might go to Harbor Freight and buy one of those $10 infrared temperature guns and see what the temps are of the various components in the engine bay after it gets 'too' hot.
My bet is on the controller box that modulates the power from the batteries to the motor.
Another bet is that you have corroded wires someplace and the corrosion is causing resistance that is causing the heat. A cheap first thing to do would be to disconnect all the high amp wire and clean them and re-connect them.
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