So after tearing it down and putting it back in I found the oil passage to the tranny was partially blocked, luckily the bearings were still getting enough oil to not seize up because they looked, felt and sounded good. After a few rides this weekend and riding it in to work today, it still gets warm but its no hotter than the rest of the engine and I don't feel the heat through my shoe and pants. I felt on a few of my buddies bikes and all seems to be normal, however the lesser heat did not fix the starting issue. I'll be getting the 24v start from icemansid as soon as he finishes building it.
Ordering parts today and will be building a few of them..
do you have any preference for the location of the relay? it doesnt have to be where i have mine pictured - it could be located further back in the trunk or even mounted outside the trunk under the tail section on the right side.