never underestimate a persons ability to screw something up. I have seen missing dowels, flywheel cut with the dowels left in, crushed dowels where the impact gun forced the flywheel into the pressure plate as the bolts were tightened. Ground down parts of presure plates to clear the dowels.
The blatent marks on many flywheels is not at top dead center but cut in there to set the gas ignition timing. Machine shop, or repair shop has one cut and waiting on the shelf, putting one with different cut marks on, not your old one. Top dead center is cast into the flywheel with a sometimes hard to see raised 0. Going by the gas car ignition marks and you could be one tooth off.