You really need wiring schematics for the engine, harness (if it's aftermarket) and the specific model/year of the bike (if you're using the original keyswitch) if you hope to get through the wiring mods the easiest way. Otherwise, you have to trace each each lead from the engine, harness & keyswitch. BTW, there's absolutely no way to do this with a schematic to decipher the keyswitch functions & associated leads...unless your knowledge base is...shall we say,
encyclopedic. Mine isn't, fortunately, Honda schematics are easy to find, which takes care of the keyswitch decoding.
Okay...now that I've hit you with the horror-story side of this task, time to break out the sunlight, wooden stakes and garlic.
You've basically got two circuits: ignition and charging/lighting, plus a neutral light lead. Thus, it's easiest to break things down, start with the known leads, then work out the unknowns via circuit tracing & process of elimination. So...
Start with the neutral lead. It should be green w/red trace and originating at the switch, at the flywheel side end of the shift drum assembly, near the countershaft.
Next up, the charging/lighting leads. There should be two AC outputs. One goes to the reg/rec input, the other to the fourth reg/rec post...and the HL circuit feed, on the keyswitch. The other two reg/rec leads are outputs to the battery(+) and (-). The problem you have here is that we don't yet know the color coding of the stator pigtail. With OEM Honda it's white & yellow. White AC feed to the charging side of the reg/rec, yellow AC feed "T'd" to the reg/rec & HL switch feed. System ground is via the chassis.
On the ignition side there should be: primary coil output, CDI trigger, CDI power, ground, switched ground. If your CDI module connects directly to the engine pigtail, then there should only be a ground lead, switched ground lead (kill switch) and primary ignition output. The ground goes the chassis, only a question of how that is routed, with this harness. Switched ground goes to the IE lead on the keyswitch and the primary output lead goes to the HT coil. Here's where the operative becomes "IF" as in "if you have wiring schematics", to ID the color-coding of everything, as well as what each post on the CDI module does, by position. With that last one, you've got no choice; electronics have no sympathy, let alone a sense of humor. If nothing else, the vendor from whom you sourced the engine should be able & happy to share schematic info with you. From that point, it'll be a matter of using the schematic to decode the wire harness...again, I'm sure the vendor will provide that info. Otherwise, the only alternative is tracing each harness lead, end-to-end, which can be done. With an aftermarket engine & wiring, I'm not gonna even make any
edumacated guesses, too risky.
Bottom line, the electrical systems of these bikes are really quite simple. Being a first-timer, that statement come across a little shaky; viewing all of those parts and what looks like technicolor spaghetti, it's difficult NOT feeling a little overwhelmed, at least. That said, it boils down to ID-ing one lead at a time. If you begin with the known leads, you'll narrow-down the choices and minimize any detective work...process of elimination will do the rest. What you'll probably find out is that the lion's share of your man-hours will be spent on "busy work" (cutting, splicing, re-routing, soldering, taping, etc) than coming up with "final Jeopardy" answers.
