So.
We have it ... maybe... narrowed down to the Blue/Red wire OR the Light Green wire in the main trunk as one of the culprits. We've tested just about everything that isn't wrapped tight as you can probably guess from the picture.
Traced the continuity up the right side through the Red/Blue wire all the way through and back down the left, then tracked the back side forward (What there was to track, anyhow) up to the front, and those are the only two consistently showing resistance.
My wife decided 2AM was too late to be out in the garage, especially since we originally planned to go up and get her her motorcycle learner's permit in the morning... oops, sorry Dawn if you ever read this thread. Guess we'll have to go on her next day off instead.
So tomorrow we'll start slicing into the wraps and figure out just where the problem is. Also we're taking the opportunity while it's naked to clean in the cracks and throw a better headlight bulb in (It looks to have the original OEM bulb, I want to put an XtraVision in it since I ride at night a lot, and the FJR is still down for the count at the moment and I'm itchin'.)
So that's where it stands. Watch us trace it in circles a few times before we find it.