Finally, I got the problem figured out a couple of weeks ago. Of course, the hacked up junkyard harness I'm using had a ground terminal ripped off in a hidden arm of the harness. Made me feel pretty dumb but I'll never do it again, that's for sure! Also, the TPS sensor was faulty so the engine would start but would only run for a couple of seconds before shutting off. I thought this was VATS at first and re-flashed the PCM a couple of times before I realized it wasn't changing anything.

Now I'm fairly sure I roasted the pedal position sensor when I cut out a big chunk of the truck pedal I'm using and welded it back together to make it fit under the dash. It's always something.