Joel,
Pull engine/trans/transfer case, to get good access.
Replace wiring harness. No easy way out,you have wiring harness damage and it probably damage the computer. Send computer out to be tested.
Other option, find a simple early ford or chevy truck.
With the soul-sucking bs you're dealing with, an old Ford with a 300 inline six will bring you a smile everyday you work it, or work on it:
