So, as mentioned before. Cleaned and checked all electrical connections, check for continuity and voltage draw. Could not get a click in the relay. I then proceeded with trying to jump the starter directly to see if she even turns over. This is what happened, big clunk in the starter and all controls went dead and stayed dead.
I figured this is it I blew the thing up. Figured I'd have to whole it to a service center 200 miles away, started to put everything back together to it's original configuration. Removed the SI fix moved all relays back in their places, started torquing bolts for side plate, as I was doing that the bike rebooted on its own, this is at least 30 minutes after everything went dark, the ignition key was in the off position. Turned the key and hit the starter key and low and behold the relay was clicking. I went ahead finished connecting the starter and tried starting it and she started right up, this is with all the original wiring. I am stumped, but not complaining.
Still can't figure out why short starting the starter shuts everything off or why she didn't start to begin with?? She is running, just hope I don't get stranded somewhere. Thank you everyone for the suggestion.