Ok, so I tried searching the boards for an answer and only kept digging myself a deeper hole. I am going to try and lay out everything I have done concisely so that the whole picture is clear.
1. Changed headlight to HID Xenon from Lumenez - everything worked fine
2. Changed brakelight to LED board from Moto Lume - everything worked fine
3. Installed LED Flasher Relay from Show Chrome Accessories - everything worked fine.
4. Changed front TS to LEDs from Custom Dynamics - everything worked fine
5. Changed rear TS to LED with running/brake lights from Custom Dynamics - blew a fuse after initial install, re-did all the wiring - everything worked fine.
6. Battery Died - did some testing, ruled out stator decided to change R/R to Shindeghan MOSFET--
charging DCV before change was 12.6-13.0 from idle - 6K RPM......After change was 12.7-13.5 same RPM range. This seemed strange to me so I had the battery tested and it was fine. So I figured perhaps I have a ground short somewhere. When I went to start looking for it, I noticed my headlight wasn't running. I looked up posts about that issue after the MOSFET install and noticed this
Headlight Not working after Install Thread...
I mostly paid attention to the posts by VulcanJoe and Denny as they seemed the most appropriate for me.
Post #7 seemed to be the answer, and if you read on to further posts it almost seems as though somehow my low charging voltage may have been related to this.
Post 7 reads
"i had the same problem when i installed mine so i wired it up like the factory with the stator lead to the jb then the r/r would not charge what i did was take the brown sense wire from the old r/r connector and solder it to the yellow wire from the small plug on the j/b. the headlight is on all the time now there is no longer a delay to turn on the headlight. hope this helps "
I misread this and tapped the Brown Sense wire into the yellow wire from the stator leading into the JB. Obviously, my headlight turned on (only after pushing start button), no other lights did, and in 30 seconds the main 30 amp fuse blew. I disconnected the wires I just put together to realize I just sent VAC voltage on the brown wire and it melted and shorted to the old ground wire in the no longer used R/R connector. So, I disconnected and fixed my cut. Now I am stumped, I do not see any other yellow wires coming from the JB other than the one from the stator. My headlight does not work at all, and I do not know where to attach the brown wire.
I think that this brown wire just needs to get 12V power to turn on the headlight, but I am not sure.
any help please
P.S. - I removed the White and Ground wires from the old R/R connector at the point where they join other wires because I wanted to clear up some space and get rid of the uneccessary wires.