Any suggestions on how to tackle this? It's a rats mess.
Basically, only two ways:
1- Replace all of the hacked-up harnesses with good, undamaged harnesses.
or
2- Repair all of the damage.
Repairing that won't be easy.
From your description, all four corners of the truck will need the wires spliced back, to the original configuration. "Color-to-color".
Then you can pull back all of the added wires to the inside, to the multifunction switch (MFS) location.
The MFS connector will also have to have ALL of its wires repaired, and restored to their original condition. Again, color-to-color.
The connector in your first pic doesn't even look to fully wired any more. If some terminals were pulled out of the connector, and then cut off for splicing, you're going to need a new pigtail connector, either new or harvested from a donor.
You'll just need to take stock first- if it's just a matter of splicing original wires back together, it's likely doable as a repair. If you find that it's impossible to find all of wires (by color code) needing reconnection, you're better off trying to find a complete replacement harness.
It wouldn't hurt, to go ahead and check around for any possible donor trucks, just in case you get lucky and find better harnesses reasonably.
Tell me what you need, for schematics, and I'll image and post them.