I had the same issue with my 2006 GT. Turnied out the compressor puked it's guts through the whole system and was locking up whenever it would cycle on. Ended up replacing the compressor, condensor, orific tube, and a few other things. Car had 17,500 miles on it, but was 42 months old. NO WARRANTY!
I called Ford, no help their either. But mine would die at a stop light when the compressor kicked on. Hopefully you aren't developing the same issue.