If it is only doing it at slow speeds, I'd richen both idle mixture screws to see if the idle smooths out. If not, I'd pull the screws and blow into the ports from the outside. Reinstall and see if that makes any difference.
When it begins to run rough, did you try opening the enrichment circuit to see if it makes any difference. Normally a dirty idle circuit should cause more problems when cold than hot since a richer mixture is usually required during warm up so if the idle gets worse as the engine warms up what I just suggested seems counter intuitive. It's a quick test though.
Another item would be to try unplugging the TPS and running without it. I had a similar situation and traced it back to the throttle position sensor. I unplugged it and never hooked it back up. Bike ran better than ever with no decel popping. You're right about heat potentially causing the coils, specifically the pick up coil to fail when hot. They usually fail open though leaving you with a dead engine or running on one cylinder.
