There's a picture of a flexplate (the automatic transmission equivalent of a flywheel) installation on
this page. It shows which direction the offset goes. It'll really only fit one way. If the starter is jamming against the ring gear, it's probably what the other guys have suggested and needs a shim or two.
There's one other remote possibility. If you've changed the flexplate from a 153-tooth unit to a 168-tooth plate, then you'll need to change the starter, too, since they have to be matched. The 153-tooth flexplate (or flywheel) uses a starter with a straight-across bolt pattern, while the 168 uses a diagonal bolt pattern. As I recall, it's almost impossible to bolt a 153-tooth starter up against a 168-tooth ring gear. But it's been a while since I've messed with different sized gears and starters.
Good luck with it.