I'm very comfortable with electronics and wiring. Your "remove one wiring harness at a time" strikes a note. That would be a very controlled approach to getting everything back to standard wiring and quality. Can you point to any resources that go through wiring harness removal? I'm guessing it's probably pick a starting point, then disconnect and follow until you get an entire harness off, but I've been WAY wrong before.
No that is pretty much it. Each section has it's own harness, like the Alternator Harness, left and right engine bay harness, frame-rail harness, taillight harness, and things like that. They all unplug in full sections for easier service.
Even the main harness under the dash is removable, just time consuming etc. Removing the dash pad can give good access, after the A/C ducts are removed for example, if even equipped with A/C.
So pick the most screwed up harness, and go from there, and work forwards/backwards etc.
As for resources, this site is a really good one for help. Look at the top under documentation, then electrical for some good information. If you have questions, ask here and one of us will be able to help. Pictures also help us understand what is going on if you have a problem.
One more question (until the next one).
Do you have a recommended approach/parts to replace the connectors between harnesses if they need replacement?