Keep at it. You are right, it should not be that complicated. I am waiting for your Eureka post; when you finally figure it out. I am betting it will be something simple in the end.
Your adventure reminds me of last year when the Smithers XS650 would only run on one cylinder and no matter what I did I could not get the 2nd cylinder to fire. It took beers at the BX Pub with Club members to brainstorm. Hans had the Eureka moment speculating that magnets in the electronic ignition were in the wrong place. We went to my shop, punched out one of the magnets and moved it. The bike ran after that, although as it turns out that was not 100% of the problem. I was actually missing 2 of 4 magnets, but moving one of the remaining magnets to a 180 degree position permitted the bike to run (with a 180 degrees of dwell instead of the 90 degrees it was manufactured for, but missing the magnets).
Peace & Perseverance, Dennis