Doug,
If your engine has been running for any length of time with the flywheel loose, the taper on the crank and the bore of the flywheel will have fretted. Also the slot for the key may have a burr on it, causing the flywheel to run out of true.
Try removing any burrs and then lap in the taper with fine grinding paste. with a bit of luck, the original flywheel will be recoverable. When refitting the flywheel, do the nut up as tight as possible. If the split pin hole does not line up - leave the split pin out - do not back off the nut to get the split pin in - this will only result in the flywheel coming loose again.
Regards,
Eddie.