I sure wish we'd talked before you started this project. That will reestablish the proper preload. If you ever do that job again first take a cold chisel and 'stake' (make a mark) the pinion nut and the yoke (Companion Flange) so that you can put the nut back in EXACTLY the same place it was when you loosened it. DO NOT OVERTIGHTEN! If you achieve 30 in/lbs STOP! and reinstall the drive shaft and be happy. I guess you might as well try to retighten the nut now and pray for the best. Those gears don't usually forgive being run out of true after their mating pattern has been established. That usually means ring and pinion failure too. You have to really be careful with this because improper preload leads to early bearing failure. I reuse the old spacer but my method is not for the uninitiated. I am not sure of what to advise you to do since I have my own way of replacing seals that I have had luck with over the years. You can try tightening the nut such that you have 30 inch pounds turning force or you can take the assembly apart and put a new 'crush spacer' in and start over. The inch pound figure describes the turning force in inch pounds that represents the friction of turning the pinion with an inch pound torque wrench with no other drag on the pinion ie: the ring gear assembly. Those crush spacers don't really like to be crushed twice. Since you apparently didn't take any measures to 'reference stake' the pinion nut you are now kinda in the woods for preload.

EDLANTA there is a 'crush' spacer between the two pinion bearings that when tightened properly gives you the proper bearing preload.

That does not describe how tight the pinion nut needs to be however. I agree that the preload needs to be about 30 inch pounds.

Pinion torque 1972 fj40