As you say, there have been many modifications to the system over the years. You have no way of knowing what's what, what's been done , and what's been done properly.
If I were you, I would start from scratch and rewire the entire truck with brand new wiring - even systems that are working now. Start with say, the headlight circuit, and work your way back. Do it by the book and it will all come out fine.
My truck had all kinds of modifications, too. The previous owner was dyslexic and got wires mixed up so headlights would only work on hi beams. There were splices and Micky Mouse connectors all over the place. He even had #3 and #4 spark plug wires reversed and he transposed characters when registering the vehicle so the title doesn't exactly match the truck ID.
Anyway, I re-did the headlights with help from this board and have been removing dead end wires and dangerous connections little by little.
I suffered a total loss fire on a vehicle from worn out wiring. It's not something you ever want to experience.
