No big deal. Just keep in mind that a hot wire from the battery positive supplies the fuse panel "hot bank" side of fuses. There are two ways this happens. One is a direct hot wire to a certain fuse panel hot bank that is not switched, I.E. you decide you want the brake lights, horn, radio to operate with ignition off. That's called "unswitched" power. The second way is a direct hot to the ignition switch and then, from the "on" terminal on that switch, a wire goes to a certain other fuse panel hot bank. That's called "switched" power. The ignition switch "turns on" the fuse panel. You can see that concept by studying the way the harness is presented and looking at the diagram and instructions. Use the gen/reg wires in another place. Cut them off and just use them as new wire somewhere as alternator wiring or for your non-original components. Don't cut those wires yet.
There could be other "non fused"/direct connect wires like to headlight switch or ammeter. Since my rule is everything should be fused, then these would need a fuse or a fusible link at their starting end. Google fusible link.
Google how to wire an alternator either 1,2, or 3 wire method, whatever you want. That is easy.
The wire leaving a fuse will generally go to a switch, almost everything has a switch. Then a wire out the other side of the switch goes to what ever the switch turns on. Like a wiper motor, a radio, heater motor, brake lights. The return path (battery negative) is metal case or housing or socket to metal. Hopefully you have enough extra fuse spots for those items that were not original equipment. If not, you can just use inline fuses. Wire up what you understand and what you see on the diagram first and then we can take up the rest here.
If I had the wiring diagram you got, I could be more sure of what I advise. But you get the gist. The horn and it's button are different than anything else. Later on that.
You don't have a major issue and the wiring will turn out OK. Just get busy so that you get more understanding as we go. You can't know all about wiring without starting to read and wire up what you understand. You can do all the rear light stuff, gauges, front lamps, ignition by following the instructions given. If they are good instructions. We are open 24/7/365.
