In alignment when things just will not work , it's usually because you've assumed something was - when it wasn't.
Example: Two guys attempted to align a motor to a pump for about two days and just could not get anything to work right. Even though they were both experienced millwrights, they kept assuming they were making some simple error. It was a new pump in a new construction project. What should have been a pump in pristine condition turned out to be a pump with no bearings. (No bearings???) The pump did not require mechanical seals. The two sets of packing provided sufficient "bearings" to allow the pump to be turned by hand; but there was a slight axial drift where there shouldn't have been. Once the new bearings (which included axial thrust bearings) were installed, the alignment process went smoothly.