I got the engine harness labeled and stripped off the truck. Now comes the fun part of opening it up and removing what I don't need. I have 2 connectors on the harness that were not hooked up to anything on the motor. Maybe they were hooked up to the body harness of the original truck? I guess I'll have to figure that out later.
Also, I think I found a suitable location to mount the PCM. Its pretty tight under the dash, with the brake bracket, steering, accelerator pedal, and TAC Control Module (drive by wire). I'll post some pics when I mock it up.