I'll make a suggestion here if I may...
Charging and ignition are two different systems. If it were me, I'd ignore the charging system issues for now and worry about getting spark to the plugs. Once you get it running, you can worry about charging. Reading above is just confusing because the idea is to get the bike running and all the talk is about regulators, rotors, stators, brushes and such.... none of which have anything to do with making the bike actually run.
So my suggestion... let's concentrate on ignition. I believe I read above that you have power to the coils, correct? If so, take the lead coming out of the coil and going to the points/condensor.... disconnect it and touch it to ground... then remove it from ground. Kinda like tapping it to ground. Grounding it charges the coil. As soon as you un-ground it, the coil should fire the plug. Tap it a half dozen times or so and see if the plug consistently fires. Does it? If it does, that's a good coil, ht lead and plug... and we're getting good power to the coil. Answers a lot of questions no? Let us know and we'll press on from there.