That diagram makes a few assumptions:
1 - you're using a car type ignition switch not the OEM one
2 - you're using a later DOHC type combined regulator/rectifier not the OEM separate regulator and rectifier
3 - battery power teleports to the ignition switch (no connection is shown, you should have a fused wire between battery + and the switch BAT connection)
The wires you care about in the engine connector are the 3 yellows, the green, and the white. The other two are the neutral switch and oil pressure switch.
3 yellows are the alternator 3 phase output, and go to your rectifier.
Green is ground to the alternator field coil.
White is power feed to the alternator field coil.
Minimum wiring would need a battery, regulator, and rectifier plus the on/off (or key) switch and a horn, headlight and tail light with brake light (and switch of course).
There's a good description for rewiring a bike using the "Santee" electrical box here:
http://www.hondachopper.com/garage/santee_wiring_instructions/santee_wiring_instructions.pdf This includes the electric start but that's pretty easy to leave out. You have to plug the case hole properly if you remove the starter motor and you still need a battery (can be much smaller though). The Santee box was just an empty metal box you could buy made to fit the frame and drilled for components, you used your scavenged electrical stuff to stuff it and rewire the bike leaving minimum exposed wiring and electricals. The bikes I've seen with them had a generic automotive keyswitch with the usual off/acc/on/start positions and fired the electric start motor on "start".
The OEM keyswitch doesn't have any "ACC" terminal, just BAT and IGN and extra ones for the oddball tail light "parking light" stuff. If you use the OEM switch then IGN power goes to everything if you want to go extreme simplicity. Santee used the generic keyswitch because they were available at any auto parts store and, unlike the Honda one, mount easily in a round panel hole.
