Ok, just because I hate it when I search problems and the OP never bothers to post up a resolution, here's the resolution to my problem:
I got the new PCM installed (bought it here:
https://www.fs1inc.com/) and, of course, the PATS system was not happy with the change.
Called in a locksmith and he turned out to be a bungling idiot and did not fix the problem. I got frustrated and since I don't need the vehicle right now, and Christmas was right there, the project got shelved until later.
Well, later is here and I called I another locksmith, a very competent one (talked to him on the phone for quite a while to make SURE he understood my problem and make sure he knew what the heck he was talking about).
Well, the guy came out and roughly 20min later she was running fine.
Word of advice to anyone with this problem: make sure the locksmith you call not only knows how to program keys, but that they know how to sinc up the PATS system to the new PCM, and that they have the proper equipment to do it.
