OK so you're running a single output DC system. The black wire from the reg/rect should have a ring lug crimped on it and be connected to the frame. The (-)black wire from the battery should have a ring lug also and needs to be attached to the frame using the same bolt as the reg/rect black wire. Take the cap out for now. Is the stock AC regulator still connected to the harness? I'm sure the stator wires no longer go to it but are the other 2 wires still plugged into it? If it is then unplug it. Also, with the reg/rect disconnected check for continuity between the red wire and the case. In fact check for continuity between all 4 wires and the case. Post back with what you find and we'll go from there.
XR650R Plated Supermoto
XR628R Plated and highly modified
CR500R Still rips after all these beers
RZ350L Kenny Roberts Special
"If it's hard to do, you're probably doing it wrong."