Ben you have more technical advise hear than a patient having heart surgery.
There has got to be something very simple that went wrong.
Bike looks clean and well done, and you obviously are mechanically inclined.
Keep looking, simple things can be the hardest to find.
By the way, what rectifier/regulator combination are you running?
What happened to start you down this road?
It was running for how many miles before this started happening?
Grounds are super important, like between battery box/frame, frame/engine, battery/frame, battery/engine, rec/reg/frame, etc.
Simple things like a layer of paint, wire pulled out of a connector end not crimped or soldered, old key switch with sloppy or dirty connection points.
Also voltage readings between when a bike is running and not may very because of poor wiring, grounds and corrosion.
Food for thought.
Don't give. You will find it.
I spent 3 weeks looking for an electrical error on a Kaw ZX1400 electrical system with a no fire error on the computer only to find it was a mechanical error. Crankshaft pulse rotor was broken, a piece of metal attached to the crank that has 20 fingers and 5 were broken, computer didn't like that but wasn't programmed to tell anyone. Stupid computers.