This has been a great thread so far. Lots of good info. What was/is the overall condition of your truck as far as corrosion goes? I can't think it would be too bad in ID, unless they do use salt out there.
My speculations are as follows:
1. Corrosion from elements over time. Also, corrosion from natural moisture, especially if it sat for 2 years outside, or on grass or gravel. Vehicles parked on non-solid surfaces are more prone to moisture related corrosion issues from my experience. I'd go over Chassis ground points with a wire brush, coat area with dielectric grease, and reassemble. Use a star washer if provided. Also check the main cables for discoloration and tightness of crimped areas.
2. Modules that died slowly from sitting so long. The steady decline can mess them up
. Or, a jump start from stone-cold dead as well. Have the battery load tested.
3. The alternator idea was something I didn't think of, but I would put down as a relevant idea. You could make sure the battery is fully charged, them remove the power wire from the alternator (tape it up, or put it in a non-conductive covering. Run the vehicle for a short time and see if anything changes. If you have a weak battery, this test won't work well.
4. Do a general inspection of wiring harnesses for pinched areas, worn areas, etc. Being that the trans and motor were gone through, it's a possibility something didn't get put together correctly. Look for proper routing near heat shields, mounting points, etc. Also look at connections to make sure they are in fact "clipped" together properly.
I absolutely HATE electrical gremlins. My hat is off to you for having the gumption to learn and tackle this yourself. Best of luck! Hopefully this brain trust (meant in sincerity) of a group can help you get it figured out. LOL