If I may add a few points aside from what has been suggested,
Check your spark plug condition if the fuel is burned properly. If you can rewire the fan to it's original thermostat sensor controlled connection it would be better in my opinion. Are you experiencing slightly elevated engine temperature? They wired the fan directly to the battery so it can help your engine cooling system. However, doing this will shorten the life of the fan itself and besides if there really is a problem with the engine cooling system and air-con then these should be restored to their near original operating condition not with odd fixes. Check the current load in the alternator whenever the Aircon compressor kicks in. If you notice a significant change in reading then I suggest you also check the compressor winding. This may also have something to do with the shutting down problem compounded by the permanent fan load being installed "rekta". Sometimes the compressor is nearing it's end and the pistons inside are already misaligned and becomes a burden load for the engine and alternator. Just my two cents.
