Completely Lost on Issue with Alternator Wiring

I purchased my first motorcycle a few weeks back, an '82 XJ650 Maxim, with a lot of custom work. It has been modified to a bobber style, which was done well. A lot of the wiring has been redone by the previous owner. Everything checked out when looking over the bike for purchase, although an issue presented itself after riding for an hour or so. The bike does not charge, and upon investigation, I found that the brown and green wires from the regulator rectifier were not plugged into the stator. I plugged them in, and started the bike. It seemed a little bogged down on idle, and the battery terminals measured around 12.6 volts. I went to turn off the bike at the key (the kill switch is not wired up), and it would not turn off, even after I removed the key. I had to disconnect the brown wire to turn the bike off. The brown wire coming from the stator measured .2 volts while the bike was running. I am completely lost. I have been referencing a wiring isse and I cannot find any wiring faults yet. I am suspecting a bad regulator rectifier. I cannot find anyone else online with this same issue. Any help at all is very appreciated.

 

Oh dear.

So not done well then.

Sounds like multiple issues. Unlike Hondas the Reg/recs on these are farilry reliable. Start from the alternator and work back. You are looking for AC volsts on the inputs into therec-reg these are normall white ires IIRC and a varying DC volts up to about 14.5 on teh output (red I think) . Try and get a workshop manual so you know what tests to make.