Just a thought... and I'm not the expert mechanic that many here are... but I had a misfire like this that I could not figure out. With a temp gun I found that it was a specific cylinder not firing. Changed plugs, checked wires, still no good on that one cylinder. I suspected a bad coil, so I tested that coil with a meter and it returned perfect numbers. Reinstalled and the dang thing still was missing on that cylinder.
Then, from a comment on an R1 forum, same exact coil, a user had a coil go bad and it wouldn't show any faults except that it wouldn't fire.
I bit the cost (I think around 60 bucks) for the new coil and it ran perfectly. I later found that Yamaha outboards use that same coil and were having occasional failures. It was just a bad coil.
Years later, the bike still runs perfectly for its current owner.
* * Just hanging around until I can ride with Petey, Mack and Rock again. Never forgotten. * *