The "not under .005" must be a typo as it should be not under .0005.
You should try each bearing by itself with the other three loose and the seal niot installed. If the crank rotates easily for each case but not with more then one done up, you have an alignment problem.
If your motor is supposed to have shims then the main bearings will have round dowel like projections on the back to stop them from rotating.
