I am more familiar with the 250sx's but they are the same beasts. Honda used 2 different stators over the years in these bikes. the stator and the flywheel need to be the same type for it to work. I do not know if mismatching will cause them to rub but it might be your issue. also make sure the stator is seated properly as well as the fly wheel. the flywheel sits on a taper on the crank. if not seated properly it could wobble as it spins.
Trikes: All Honda: 84 250r, 85 86 and 87 250sx, 84 and 85 125m, 79 82 84 and 85 110's, 73 us 90 and 77 atc90, 75 atc70
Cycles: Honda: 71 cb100, 78 cb750 coming soon cb750 trike. Yamaha: 67 yds 3 (250cc, 2cyl, 2 stroke), 82 750 SECA
Other toys: Chenoweth VW sandrail dune buggy, old race go kart, racing mower, 76 Arctic Cat Pantera 440 snowmobile
KEEP IT ON ALL 3 OR AT LEAST 2 AT A TIME