2007 Ford Fusion Problems?

Hi,

I recently bought a 2007 Ford Fusion for pretty cheap because the A/C doesn't work. I figured I would be able to fix it pretty easily but I was wrong. I have bypassed the A/C clutch relay and then everything works just fine so the problem must be before the relay. I am starting to think it might be the PCM because I get a "check charging system" warning before I start the car that disappears after I start the car, and also the anti-theft light continuously flashes. With both warning lights it seems the normal symptom is the car not starting or only running for a short time and then shutting off (from what I've researched online). I am wondering what else besides the sensors could be the problem with the A/C? Also, if the car starts and runs fine, is there any reason to be worried about the warning lights I am seeing?

Thanks in advance for any suggestions!
Added (1). Oh and one more thing. I found a used PCM on ebay for roughly $50 and was thinking about just trying to replace the PCM. Then I did some research and found that I might have to reprogram the new PCM to work with my car? Anyone know if I actually need to do this?
Added (2). I have also switched the relays and the relay works just fine in the spot for the windshield wiper relay.

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