The stock wiring diagram may look like a plate of noodles but it is actually pretty simple, at least in comparison to a new bike with all the computer stuff.
You have to get a wiring diagram, the original Honda one is best and should be findable online. The others, like colored or whatever, all simplify some things or just skip them.
See what harness wire color each ungo wire connects to. If there are two the same, they just get spliced together. Otherwise check on the diagram what the wire does. The box is going to have a power and ground wire, maybe a switched power and a direct battery power also.