Electrical Gremlins....
Are you coils in the center of your engine? I had something like that on my Shovelhead. If there is a cover that goes over the coil make sure none of the wires are coming into contact.
My shovelhead was wired by someone I knew pretty well. Those damn crimp connectors suck! You may have a loose connection or two!
When I wired my Duster I cut every one of those damn plastic/vinyl insulators off. I then used a ratchet crimper and heat shrink on every connection. Something you may want to consider on your bike. You could also you some silicone sealant prior to heat shrinking.
Here is a cycle terminal website I just found. I like how the terminals and the and insulators are separate.
http://www.cycleterminal.com/bullet-terminals.html
Here is a complete wiring harness from JP cycle. I have no experiance with it but it seems pretty decent. This may be a good way to get rid of the wiring issues once and for all!
http://www.jpcycles.com/product/381-001
Good Luck!