Did you pull out the idle and main jet when the bowl was off? I know you said it was clean but the PO may have been chasing a this problem as well.
More than once I ave been surprised by how BAD todays fuels are They leave concrete hard deposits that a soak in Berrymans won't even loosen up. A cheap set of jewelers drill bits will let you use the appropriate size to clean them out by hand without enlarging them. Might as well run them through all the holes in the emulsion tube as well. A Welding tip cleaner set works ok too, but I prefer the bits.
That said, if the problem is following the cylinder ignition swap, that narrows it down greatly. That plug wire, the one coil output tower, that plug... Pull one off and try to start it that way. No start means that the wire/plug/tower, starting and running the same mean the opposite one is the issue.
Sounds like you are on the right track...
If indeed it is just firing intermittently on both cylinders (warm primary tubes clue) I'd look into the cam sensor. Disclosure: I don't know tubers well... it might have a crank sensor? Whatever it is that fires the coil, or a bad connection between the 2 is what you're looking for.
Good luck bro. I happen to be in your town until wednesday, staying just south of you in Old Town, Muahahaha. If you want a hand I can try to make some evening free time and swing by