Learn Me Angry Pixie Arson Defense. (wiring questions)

I've finally come to the point that I need to learn how to wire an entire vehicle from scratch for the first time. Something has gone so wrong that the fuse box is irrelevant and it's definitely a fire hazard. I really don't see anyway forward other than starting over. So I'm asking for help planning a new harness.

The victim in question is my constantly annoying D350 that despite me threatening to do everything from sell it to LS swap it, is probably going to stick around in close to it's current form for quite a while.

Things I'm considering:

• The current location of the fuse box is extremely annoying and has to change. It's mounted on a removable panel on the dash under the steering column. I haven't yet decided where the new one is going to go, but it's definitely not here. Current best guess is behind the glove box.

• Currently has a separate voltage regulator mounted on the firewall in a location that I believe is causing rain water to hit the back of it and cause premature failures. I've thought of either switching to a GM alternator with the regulator built in, or at the very least relocating this regulator. I've noticed that it looks like the other trucks have this regulator further down on the flat part of the firewall, but there's a giant 12V Cummins in mine that makes this location unreasonable.

• It's an old dually so the cab lights and fender lights have to stay, but I have considered switching them over to LED. The sealed beam headlights also have to go, but I want to find a good set of conversion housings that don't look ridiculous.

• No plans for power windows or locks, but a stereo is probably in the cards and AC is staying.

• I've looked at universal wiring kits but it seems like most of those would require just as much if not more work to do what I want than starting from scratch.

• Ultimate goal is reliability, ability to trouble shoot, and the ability to add onto it later if I decide something dumb needs to be added like an electric water pump for a water to air intercooler. (Current best plan for adding an intercooler while keeping the '89 grill intact, I'll deal with that stupid later)

My other question is if anybody has a good source for the materials I'll need for this, or some decent reading material on this subject.

I'd like to do this as cheaply as I can get away with and still end up with something safe and reliable.

The aftermarket harnesses, while a bit of work to install, should still be easier than doing it yourself. Painless, American Autowire, Ron Francis and others make universal harnesses. My Dad's 53 Mercury has a Ron Francis harness and it is a neat setup. It was already installed but is much cleaner looking than some of the others.

As for LED lights, you may find your current clearance lights on the fenders are just trailer clearance lights, so there are readily available LED ones that will go in their place. There are many options for headlights that will fit in place of the stock ones. I would get ones with replaceable bulbs.