I hope you did NOT disturb that pinion nut. It is used to set the bearing pre load on the two opposed tapered roller bearings the pinion runs on. Over tightening it puts too much preload on the bearings and they will destroy themselves in short order. There is a crush spacer between the bearings, you cannot loosen the pinion nut after you have over tightened it except by pulling it completely apart and replacing the crush spacer and properly crushing it to the proper preload, which is measured by rotating the pinion with the axle shafts removed, and a extremely low range inch pound torque wrench, beam type, probably less than ten inch pounds max range on the tool. The manual will have you measure the rotating friction of the pinion and tighten the nut until the preload of the bearings is reached, as determined by the rotation torque. Its close to a black art and not something to mess with.
Please don't willy nilly try to tighten the pinion nut.
If you have to replace the pinion seal, you punch mark the nut the end of the shaft and the flange, and count the turns off, exactly. Reinstall it, exactly to the same spot and no more than a thousand or two tighter from the nut to shaft punch marks, that could even be too much. Easiest way to hold the flange is take a piece of flat steel or angle iron and drill it for a couple of the flange holes, and bolt it to the flange, and allow it to rest on the leaf spring. Makes it a one man job.
Hope you haven't ruined that new rear end.
Charles