Oh God, I hate to mention this because it's so likely not happening that it will make me seem rude for even mentioning it. I've combed over this thread pretty extensively now and have come to the conclusion you are extremely familiar with your bike. So familiar, that I can imagine the possibility of an opening for overlooking something because you are so familiar with where everything goes that you might miss something that appears in the right place, but isn't. Is this starting to sound like one of those online stories where it takes forever for them to get to the point? If so, you can take that as indication of how uncomfortable I am to mention this possibility, which, as far as I can tell, has not been mentioned in this thread.
Here goes: Have you carefully checked that your plug wires are not reversed? There was a mag replaced and the engine was retimed. Maybe, in the past, you've always timed on the nearside cylinder but forgot and timed on the offside. If you were used to, for example, the bottom pickup going to the offside, now it would have to go to the nearside. Did you check the plug wires by verifying against the position of the brass on the slip ring as the pistons approach TDC?
OK, that's all. Please don't travel to Chicago just to kick the crap out of me.
Richard L.