Many seem to have this problem (at least that talk about it). When I bought my 14.5 amp 3 phase stator with a new rotor from Matt I used a cut-up plastic water bottle that measured 0.01" thick to make sure I had the proper clearance between the rotor and stator (I have Matt's e-start so the stator mounting is different than stock). I tested it at idle and the clearance and charging was fine. I went for a ride and noticed that my IC charge warning light was showing no charging after a while. When I got back home and pulled the stator it was completely melted and destroyed. I had Matt turn down the rotor 0.01" all around and installed a new stator. Same installation procedure with no issue at idle, but when ridden it was rubbing again, but not as much. I used a Dremel tool with a sanding drum to clean up the inside of the stator and remove a little of the epoxy material all around being careful not to damage the magnets. Finally all is well, but I would guess that I now have about 0.025" of clearance and still get good charging. I measured the crankshaft with a dial indicator and am not getting any noticeable deflection when manually turning it, but who knows if there might be some when it runs and heats up. Maybe a slight bearing issue, although the engine has less than 1,000 miles since completely rebuilt by Classic Bike Experience.