Just out of curiosity: how did you store this crank while it was out of the engine? As in: lying on it's side or on end or hanging with wire or how??? Just wondering....that is all.
do you have a dial gauge? i would set the crank up with a dial gauge and rotate slowly to check the straightness... as said before is sounds like a warpage or bent crank.. (altho odd if you stored vertically) i've only know cranks to bend laying down..