the only way the rotor/stator gap will be good when the engine is running is if the rotor is well centered on the crankshaft when the gap is set up. If you have your rotor/stator gap well adjusted now, slowly rotate the engine and check the rotor/stator gap in the 12, 3, 6, and 9 o'clock positions to make sure. If the gap doesn't change much, you are pretty well centered and well spaced, so you are good to go.
Is this too obvious to mention?... I didn't mean the comment to be condescending....