Re: running so oddly...?
Simply filing away material from the woodruff key is not the right way to change ignition timing. How are you confirming that the rotor (magnet) is not moving on the crankahaft. Simply tightening the nut will not keep it where you put it. If the key is now more narrow than the key way it's a good bet your timing is all over the place; advanced and or retarded. You said that the problems started after you worked on the woodruff key. That tells me something. Install a new key and try it. If the issues go away, you've found the problem.
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