Pics are good. More clarity on the Reg/Rect wiring would be better.............I'm not an electrical guy, but it seems on the Reg/Rect from Mikes there should be 2 sets of wires...3 Yellow in one set with a plug, 1 red and 1 green on the other set of wires with a plug..........No Blue.
Here is a link to a Pamco thread, with wiring diagrams for a Genuine PAMCO and PMA set up, Post #3 has the diagrams. Battery can be in place of a capacitor..........20amp fuse should be before the ignition not on the Reg/Rect red wire.
http://www.xs650.com/threads/pamco-ignition.46859/
Some one with an electrical background may chime in, not really my forte .............If not a Genuine Pamco Ignition then there may not be a warranty and there have been some issues with
MikesXS Charge Ignitions ......
THESE ARE NOT PAMCO'S..................
Edit
that being said, on your wiring diagram, the Reg/Rect has green and red both running power........I don't think that is right............also refer to the fist sentence in this paragraph.
Not a lot of love for MikesXS XSCharge Ignitions on here .......... while he was selling the pamco he got it reversed engineered and started to sell his Pamco Copies and now PamcoPete has stopped making his Pamco Ignitions............