Bee, my 2 cents' worth:
1. Your voltage regulator appears to be broken off. PM me your address and I'll send you one of my spares.
The rest of the wiring so far appears to be misrouted and maybe a little skinned up, not certain death.
2. Look closely at the clips that hold the fuses: if they are corroded or a dark chocolate color, they won't work (that's the old chromate coating, peeling off). When this happens, they heat up the fuse ends and melt the fuses when used. You can get a new NOS clone from Partsnmore.com, or I make a more modern style unit that uses modern automotive (ATC) fuses.
3. If you install slightly shorter rear shocks, like I did for the bike on the cover of my book, the bike becomes far more manageable. We used shocks intended for the CB550 (12.5" long) and slid the front forks up about 1/2" in the triple trees, and the owner, with his 26" inseam, could get both feet flat on the ground. I also installed a 110-90 rear tire, which is 9% smaller diameter than stock, to help.
4. Chances are, the brake hoses are cracked from age. When you replace them, install the hard-cover type found at
www.Z1Enterprises.com (among others) that are made by Goodrich. They increase the stopping power noticeably on these bikes. Keep in mind, "terrible brakes" here is a comparison to 1990+ brakes with highly-sintered pucks with 2x pressure magnifiers and cast-steel discs (that rust), and remember that nearly 1,200,000 SOHC4 bikes were made and ridden with these brakes for decades: it's sort of a relative thing! If you're going racing, yeah, then go get some Brembos for it...