Are there special tools for aligning the gears in the front axle?
--In case you need to remove the pinion--
The pinion shaft has an inner and an outer bearing on it, both of which are pressed on. So you have to drive out the pinion from the differential case (which removes the outer bearing at the same time), then use a puller long enough to reach the bearing from the end of the pinion shaft to get the inner bearing off.
Pinion depth is set by a simple shim during reassembly (before the inner bearing is pressed back onto the pinion shaft). The manual doesn't say whether shims of different thickness are used - it simply says "install pinion depth shim on the pinion gear shaft". I guess maybe pinion depth needs no adjustment, since doing so would be a huge PITA (you'd need a new crush sleeve and have to remove/install both the bearings every time you wanted to try a new shim thickness).
When it's time to reinstall the pinion nut, you simply tighten it until you get a drag of 15-20 in*lb on a dial-type torque wrench.
There is NO mention of adjusting the pinion depth! I'd like to think that's because you don't need to if you're using an OEM ring and pinion, but I don't know for sure.
There specialty pullers which can be improvised using some iron pipe. There's a "special wrench" that holds the pinion flange while you remove or install the pinion nut, but I think that would also be easily improvised.
--This section for differential only--
To align the differential after a bearing replacement, there's a whole procedure of adjustment. I'm attaching a picture of the spanner to this post, along with a picture of the bearing adjustors where the spanner is used. That special spanner looks pretty simple - you might consider making one rather than buying it.
You need to check backlash too, so a dial indicator might be necessary (although the procedure in the service manual shows how to do it without any dial indicator).
It's not a difficult procedure, but you will need a service manual to do it. Lots of steps.
Ryan
[Images courtesy the 2003 factory service manual]