No real experience on newer bikes [my newest is a '71 BSA Thunderbolt], but here's a few long shots...
Any chance of an excessive air leak into the #2 intake tract?
I've had duff coils on my Ford V-10 that wouldn't trip code on the OBD 11 or some scanners, would miss under light loads but seem to fire fine otherwise, change 'em out and the driveability problems went away.
If you can, do any compression checks or leak downs hot, I've had small cracks in pistons that didn't really open up until they got hot.
Yes, keep us posted on what you find, this one has me curious.
Ed