I am far from educated to figure out how reversing polarity might have affected engine running, assuming the blown fuses were replaced. We would need lPeterssen here...
But if I had suspicion that the current engine running is related to polarity reversal event, and if engine runs well cold and has issues running hot, and if you try to figure out how it might be related to electricity, I would then try work with electric components related to that. That would be relays responsible for switching on cold start valve and cold start solenoid. I would start the engine and then disconnect both of them.
If you have the FIP cold start solenoid in your car, I would check if it is not stuck in working position (remove it and hook it to voltage, see if it is working).
But I am shooting from the hip here...