I ended up doing something similar to this on my build. I didn't really set out to replace all of the wires, but I ended up replacing about 90% of them myself. I'm an electrical engineer, so that part was fine. I ended up using the factory fuse block, and kept the factory wiring schematic. If I were you, I'd get a few colors of wire and try to replicate the factory wiring. It's worked on our CJ's for a long time, so in most cases its completely satisfactory for our needs. I'd do the headlight relay upgrade, and maybe convert your choke to an electrical one that functions off of an oil pressure switch, but other than that I'd stick to factory. Depending on the state of the engine, and whether or not it is HEI, you may not have as many wires to deal with as you think. There are a lot more (in my CJ) behind the dash for the factory speedo/ from the steering column. It's definitely doable, so good luck with your CJ adventure.
1978 CJ5 - 304 V8 - Twin Sticked and sitting on 35's
2010 JK- Rock Krawler 2.5" on 35" KM2's