My advice would be to lap in the taper, then do the nut up as tight as you can get it, and, if necessary, leave the split pin out. Backing off the nut to get the split pin in was probably the reason you had problems shifting your flywheel - the slight movement caused the taper to 'fret', then the irregular surface hampered the flywheel removal. This method has always served me well, and I've never found flywheel removal a problem.
Regards,
Eddie.