So the problem is diagnosed and fixed.. And the answer probably won't really help anyone else if they have this problem, because this kind of stupid crap only happens to me.
The short of it is, the wire that runs from the pcm, to the fuse box to the alternator, that gives a signal to charge, had some "cuts" in it INSIDE the wire loom.. It looked like it was just some wear on the wire's coating.
This in turn shorted out the computer which made it so that the POWER side of the computer no longer activated the positive side of the transmission relay or charging relay, IE no charge. (it also fried that single part of the PCM)
The new PCM I had is from a truck with anti-theft built into it, and those PCM's CANNOT be reflashed for use on another truck.
We basically taped up the damaged wire, then wired the relay to be kicked on by another key-on power-on circuit. Charging & trans works fine now.