Ben has a GS500. Or five.......i can't keep track.I'm at a little bit of a loss on this Ben. Could it be a weak connection around the spark plug boot or something?
Crazy idea but do you have a timing light (car type strobe light)? Clamp it around a plug lead and rev the bike up and down and see if the strobe misses beats or if it's steady when the motor coughs.What I'm trying to come up with is a cheap way to prove that it's electrical.If it does miss beats, then the next question is it a partial break in a wire or a short between a wire and the chassis somewhere - or maybe it's a broken plate in the battery. Try a different battery and see if it makes a difference.
GS500 has the same sort of ignition as a 450 with electronic advance and the rotor is a large diameter rod with a disk on the end with a single protrusion to trigger the pickups. Yes? The air gap on those and the earlier ones should be similar on both sides. Try loosening the pickup plate and move it slightly to even the gap up. The advancer was presumably the same part but with the tab cut in a slightly different place. I like to see 12v at the coils with it not running and 12.5 with the engine running. If you have much less than that, you could fit a relay into the system to reduce voltage drop. That doesn't explain why the misfire is so rev specific though. What do the plugs look like when it does that? wet and sooty? It almost sounds like a carb problem rather than ignition, but let's eliminate the obvious things first.
Definitely do a plug chop at whatever throttle opening causes the issue, that will tell you what the fueling's doing at that point...
This has me stumped as ever Ben. But the coils would normally break up at higher rpm's and shut down when hot. You said it fired out the carbs and the plug were not rich? Might be just the mixture screw, slide cut away, bottom edge of the needle jet, etc.