Hy truckernix, it is common practice to adjust the position of a seal in a bore (if that is possible), or buy a thinner seal in order to avoid a worn area on a shaft or in this case the pinion yoke. You could use the yoke with the seal in place on it to push the seal into place, once the pinion shaft threads are exposed you could thread the nut on to push the seal into place, you will have to push the seal slightly farther into the bore that the yoke will push it to come up with a running clearance, you could use a large socket or an appropriate size of tubing or pipe to finish the seal installation, hope that helps.
