I'm not sure I follow your troubleshooting methods..."
Wiring problems are very straight forward, a VOM will track down any short or open...
Have you checked anything using a meter?
Start at the beginning the battery is it in correctly Negative chassis ground... The charging system seems to be only 'part' of your problem... leave it disconnected until you get the thing running, carb set up & coil producing good spark... then work at the charging system...
It sounds like you may have introduced additional & unrelated problems all along the way.
Welcome to this fun and at times, even helpful forum... :smile:KennyV