Try removing the starter and see if that makes any difference. The reason I say this is because a buddy of mine who ended up working on a 67 mustang and the whole thing is a basket case. He had the same thing. At some point in its life someone had taken out the tranny and when they reinstalled it, somehow they used the wrong torque converter/bolts and one stuck out just far enough it was hitting the starter. When you would bar the motor over you could hear a clunk sound. Placing my hand near the back of the motor you could feel it striking the starter. Dont know if this helps. In our case it was one of those "didnt know that was possible" moments.
Good luck.