I used brand new Timken bearings as my set up bearings and it worked like a charm. Using used bearings for set up introduces clearance issues.

EDIT. Set up pinion bearings were slightly honed out so they easily slide on and off the pinion without the use of a puller.

 

Not sure the method you used to remove the pinion bearings but a bearing splitter and a press take approximately 60 seconds and there's no pressure at all applied to the bearing. Maybe you used a socket to pound it off the pinion? Lol