Quit looking at the diagram if you're going to wire it up from scratch - the current diagram isn't much use.
The only important stock bits from that diagram is the charging system, and the ignition system. But even those are basically generic.
You can I think boil a wiring system down to a few basic sub-systems.
Charging
Ignition
Lights
Starter
That's it. Nothing else is needed.
The Charging system involves the stator/rotor, regulator, rectifier and battery
The Ignition system goes from the Battery, through an ignition switch, to the points or electronic pickups to the coils
The Lighting system goes from the Ignition switch to the headlight, brake light and turn signal switches, to their respective light bulbs.
The Starter system is dead simple - heavy lead from battery to solenoid, from solenoid to starter motor. Regular 18ga wires from solenoid to starter button.
Not sure I've missed anything. If you want dummy lights, they just connect to the appropriate points in each subsystem. But if you need a flashing lightbulb on your dash to tell you 2 other lightbulbs are flashing on your signals, then maybe it's time to quit modifying bikes

I can somewhat appreciate a neutral light, on some bikes, but I've lived without one on my XS for the last few years.
So copy the basic charging wiring diagram from the stock one, but it's a cluster of wires coming off your alternator going to a plug which connects to the regulator / rectifier and battery. I used the stock wiring connected to my XS stator and the stock harness plug and custom wired from the regulator/rectifier unit I used and my battery to the other end of the stock plug.