Not sure if it was mentioned,but flywheel will bolt on six different ways and five of them are wrong. Any noticeable vibration when it was running before? There is also a remote possibility that it has a 64 or earlier crankshaft rather than a 65-6...different seat for the torque converter to mate with. Just a couple more things to look at.
Yes, the flexplate will bolt on in multiple different ways. However, there is a 7th hole that is supposed to align up with a hole in the back of the crank that defines the orientation. Not a good design....should probably have been a dowel pin or some other method to preclude bolting it on wrong.