Have you checked the PTO shaft where the splines mate with the pump and drive? If the splines have been damaged, they may not slip fully into the mating parts. If it seems to be seated solidly, it still could be bound up on a damaged spline.
Also, be sure that the bearing is fully seated on the shaft.
I once had a rear axle that used a different bearing than the auto parts store specified for that model truck. After the second bearing "failure" (movement of the rear wheel in and out) I measured the recess in the axle housing and discovered that there was a wider bearing that actually had the proper width.
In theory, the only thing you really changed to affect the position of the bearing cap is the bearing itself. Compare the width of the new bearing to the old one. If it is the same, then the position on the shaft is the variable. If it is in the same position, then the shaft isn't seating fully in the pump or the drive splines.