Ok, I got everything sorted out.

The guy that fixed me up said that I had everything right, I just hadn't bypassed the VATS (as mentioned above) and the door locks were trying to trigger on a negative charge instead of a positive one. He swapped out my bypass module for one that was set up with the right door lock configuration. Not sure what kind it is, but apparently the other bypass module that I picked up was less specific to my truck year and model, and to make it work I would have had to run a pair of relays (one for each door).

Thanks again to those who helped out, glad to be done with it.

Now I'm going to start shopping for a new audio setup!