Most of the differentials used in our Turbo Diesels have a collapsible spacer (“crush sleeve” between the two pinion bearings, not a solid spacer or shim. You must be careful not to overtighten the pinion nut on re-installation or bearing preload will be excessive. First brush and spray clean the area of the pinion nut and companion flange. Measure the depth from the end of the pinion stem to the nut with vernier calipers. Put a paint mark from the center of the pinion stem outwards across the nut and onto the flange. Then, remove the pinion nut by holding the flange with a piece of bar stock or angle iron that you make up to bolt to two of the positions on the flange, and a ¾” drive socket and breaker bar with “cheater” pipe to turn the nut. Pull the flange and replace the seal, putting a good grease on the lips of the seal and the surface of the flange it rides on. Replace the flange and nut with blue loctite on the threads. Carefully tighten the nut so the paint marks line up and then just a little bit more, and check with the calipers to be sure you aren't one thread away from being tight. It is common for the tapered roller bearings to take a “set” and you think the nut is tight when it really is a thread off from being tight. If you can turn the flange some while tightening the nut, that will help keep the rollers aligned.
If you are experiencing any leakage at all with conventional lube, the leak will probably get a lot worse with synthetic lube. The manufacturer has to use additives to help keep the seals soft and swollen with synthetics, and the additives often don't work as well as the natural ingredients of a petroleum-based lube like the excellent Lubrication Engineers #607. I use that lube in all my differentials, including the high-friction 9” Ford type, which exhibits gear scuffing with many other lubes in heavy service. Mag Hytec can sell you that lube, if you decide on it. If you have another preferred source for lubricants, see what they have that helps keep seals from leaking while providing superior lubrication and scuff resistance.