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.
I think if it were me, I would move the good pickup coil back to the front cylinder and purchase a new one for the rear. This will keep your wire color code per schematics.
I would also do the pickup coil mod to .020", and put in the iridiums.
Part# 59026-1062 COIL-PULSING
Better check that part# with the part distributor.
Edit: Not sure, but the pickup coils may come as a set.
If you run out of options, get stumped, or are tired of swapping parts around, iridium plugs require less voltage to spark, so they may keep you going (at least for a while) until you have an outright failure which may be easier to diagnose.
ok, i found out that there was a short in wire /plug for voltage regulator, repaired that and bike now has 12v to all coilsbut now it will not charge. if i shut it off i have to put a charger on it to start it again. whats chance of alt/stator still good?
Front or back of the shaft? I'd might pull it and give a good lubing at both ends. And check the final drive fluid level. Whine to me normally indicates gears and not spline. Road a V-Star 650 and that thing had a lot of gear whine. The guys on the net say it's due to having straight cut instead of beveled gears. Anyway didn't but that V-Star... Got my Vulcan instead.
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