Hi DrDoug. That's a lot of stuff. I'll give you my opinions based on my own experience.
Anyway, here goes:
Fuel: If the tank is not rusted completely out, I would try to clean it out and coat it with one of the DIY sloshing compounds. I have done this twice and both tanks lasted decades. One had a couple pinhole leaks and the other had some surface rust inside. I think I used the Eastwood product buyt I can't recall. Each tank lasted 20-25 years. In each case, new tanks weren't being made at the time.
Don't neglect the fuel lines themselves. They could be rusted up on the inside or full of crap. Inline Tube might make a pre-bent line for your truck. I've used them on my truck and Cadillac and they are perfect in all respects and fit like they should. Much less work than forming your own fuel line.
Electrical: Switch the + and - on the battery and you won't have any trouble. Be sure to switch the + and - wires on the coil as well. Wire to the points should be same as ground. I'm pretty sure nothing on the dashboard cares which way the electrons flow. If I'm wrong, I'll soon be called out.
Edit: He was. 
See Rich's post here just added a few clicks down this thread. 
~ Peggy MThere is nothing wrong with a 6v system. I use my truck a s regular transportation and I have never had any electyrical problemss that have anything to do with 6 or 12 volts. The key to 6v systems is to make sure your battery cables are 00 gauge and that all your ground cables and ground connections are clean and tight. My starter spins over as fast as any modern 12v car.
My 6v sealed beam halogen headlights are as bright and shine as far as any 12v vehicle I own.
Don't switch to 12v out of fear. Switch if you plan on adding a bunch of modern electrical stuff.
My truck, Cadillacs, and Galaxie 500 all have DC generators and they do the job just fine. No need to "upgrade" to an AC generator (alternator).
My philosophy is/was to use what I have and not try to reinvent the wheel. If your truck were already gutted and you were starting from a blank slate, by all means install 12v w/alternator.
Glass: My windows are all bubbly in the corners and edges. I have no plans to replace any of the glass.
Wheels: I have 16" General tires on my Packard. Those are awesome tires. I had 16" wheels made for my truck to get rid of the horrible 15" trailer wheels that were on my truck 3 years ago. They look great. The larger diameter wheels and tires look a lot better under the fat fenders and also allow you to drive a little faster on the highway without excessively revving the engine.
Brakes: My truck has Huck brakes all the way around. I installed new wheel cylinders, shoes, and master cylinder and have been driving for thousands of miles without issue. There is nothing really wrong with the Huck Brake design. It's just different.
My goal was and is to drive the truck, not work on it. If the parts that are on it are serviceable or if the system in question is generally sound, I see no reason to "upgrade" it. It's a lot faster and easier to replace or repair parts and systems with stock components.
I also like to be able to look at the shop manual to see how things are supposed to be. I don't presume to be more knowledgeable than the engineers who designed the vehicle so whatever they say goes.
