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!
My coils are like mounted like yours but I lost the coil cover when I moved. A lot of the bike was soldered. Where there needs to be connectors I will be using Weatherpack connectors. I have a pair of open barrel crimp pliers that I am not to fond of, the replacement ratcheting Delphi pliers are in transit. The company that made the harness has yet to get back to me about a manual, they do not know which harness I have. I am going to connect an unused LED by the tach into the ignition circuit. The wiring from the power module is good. As long as the power is on the LED should be lit. What I am suspicious of is the circuit breaker for the ignition is tripping for some reason. This circuit is what is supplying power to the kill switch, which then sends power to the start button and the coils. If this breaker trips it will take the power from the coils as well as the starter.....and the led that I am wiring in.
Every time it crapped out the other day the starter was dead for a few seconds as well so....

Thanks for the links. I very well might be replacing the harness soon just to get rid of the disaster that is on there now.....