I discovered a similar problem after I crashed. During dis-assembly, I found that that the center connector was fried. I did the standard stator test, comparing the AC voltage across the wires, and it was all good. Since the bike was charging OK before the crash, I assumed it was loose and had been arcing for a while.
My solution was to do the cut and solder routine, removing the connectors themselves, soldering the wires together and eliminating the connector.
Bike is charging perfectly now, reg/rect wasn't the problem, stator wasn't the problem, connector was the problem.