So I have the aftermarket 4-into-1 wire loom colors translated to the Honda stock wiring diagram colors, including the lower wire loom. I know where everything goes and I'm ready to wire the bike up. Maybe when the garage warms up a bit.
The only thing I need to find in the boxes of stuff from the PO (or order new ones) are the rear brake light switch and - new to me - a small two-pronged silicon rectifier that is part of the clutch safety system on the "F" models that prevents the solenoid from working if the bike is not in neutral.
Thinking out loud, in the electronics tray under the seat will be the battery, the starter solenoid, the winker switch, the small two-pronged rectifier, and the fuse box. I'll have to see if I can get the stock connectors stuffed in there or I will have to modify/streamline the loom, I assume by eliminating the bulky plastic connector housings. I will mount the Rick's combined reg/rec somewhere it can get some air, perhaps under the tray. I assume drilling holes in the tray to allow me to use zip ties to secure components is an approach to prevent shorts from shifting electronics?
The PO really did a job on the end of the alternator/stator connector. All the wires are there, he just changed it from the 9-space/7-wire male plug to a smaller 6 space/wire female plug and terminated the neutral switch and put a female blade connector on the white wire. He also added one power line with two connectors.
Probably not worth my time to reverse engineer, but I was trying to understand what the PO was attempting? Eliminating a part of the lower harness and go right to the old Reg/Rect? See image below. I plan to put everything back as it is supposed to be unless, as stated above, I need to streamline parts of the harness to make it all fit in the tray under the seat or elsewhere.
PO work pictured.