Brass hammer and brass drift. 2 indispensable tools in my gear setup tool box. Also I do not use the old pinion nut I got get a normal nut to zip down when doing a setup.
I know I am late but for future reference the pics above of the upper pinion bearing are completely normal. It is typical to need to tap the upper bearing down on the pinion then use the pinion nut to go down the rest of the way. Hence the reason I use a non locking boring everyday nut on the pinion