To me it sounds electrical. Start cheap. Consider swapping the pickup coils to see if the problem moves to the front cylinder. Check resistance of both to see that they fall within spec.
Also, while you're in there, consider the pickup coil mod to bring both pickups to .020" of the flywheel. I would check for spark with a timing light on all plug wires. Anything suspicious would get further inspection.
After getting the bike warmed up where it is failing, run it in a dark area to see if you are leaking a rear cylinder spark to ground somewhere abnormal.
Not that it is related, but if you don't have iridium plugs, consider putting them in.
Worst case, the IC ignitor may have some thermal expansion issue.