I am almost starting to wonder if there might be a metal dye useful to highlight the marks that are almost invisible or are invisible to the human eye on the factory cranks especially. The grain of the metal has to be altered by the original striking of the mark I would imagine. As Tom mentioned if your engine ran fairly smooth with the old flexplate I would not hesitate to put your modified flywheel with it"s now matching imbalance on your own marks. Seems the only sensible thing to do at this stage.