ahhhh, now this is starting to make more sense. many engine control modules disable the A/C when the engine is overheating.
My prediction is that the waterpump is causing your overheating problem, and when the engine is too hot the A/C is disabled causing your flashing light. The A/C condensor is mounted directly infront of the rad and it can throw a lot of heat towards the rad which would only make a overheating problem worse.
Good luck!