Hi,
The ball bearing on the shaft at the front of the transmission should be tight on the shaft, and come out with the shaft.
It is pressed on the shaft, and should have a snap ring also on the shaft.
Below are pages from the Cub parts manual showing it, if you need them.
http://www.farmallcub.info/manuals/cub_ ... 007-08.jpg http://www.farmallcub.info/manuals/cub_ ... 007-09.jpg Since you have it apart, be sure the shaft you use has a good PTO pilot bushing, in the rear of the shaft.
People have said on here that their PTOs didn't work right when the bushing was wornout.
TM Tractor has a new bushing, if needed.
Grease the front end of the clutch shaft, that goes in the pilot bushing, and front end of the PTO shaft, that goes in the PTO pilot bushing, when putting it together.
The side of the trans front seal retainer with the bulge faces into the trans.
Maybe you knew this info already.
Below are pics from TM Tractor of the shaft and bearing, and the pilot bushing in the rear of the shaft.