i suspect that isn't too bad. the bigger potential problem is the flywheel/magneto. ya need to check the inside surface of that and the rare earth magnets that are impregnated into the inside surface.. if the inside surface is bad, this could ALSO indicate CRANK damage. We wont' go there right now. If the engine vibrates worse than before, then you have a serious issue.
for now, put the new stator cover on with that stator mounted. start the bike with the seat off, and put a multi-meter to the terminals. you should see 13.5vt right away, then as you rev, it should start to climb. Continue revving up to 5000 rpm for awhile, holding 5k, it must get to 14vt.. if it won't, or if you charge the battery for a little bit, and it still can't hold 14vt, the stator is bad. i just don't think that is that bad though