So it sounds like you have two questions, pinion depth as controlled by the pinion housing shims and pinion assembly. First, you'll want to assemble your pinion bearings, spacer and housing. You'll want access to a press with some arbor plates and some pushers for the outer bearing. Press the inner bearing onto the pinion, install the solid bearing preload spacer and shims, install the pinion housing and then press on the outer bearing. I started thick on my preload spacer shims and then measured the end play of the housing while still in the press and under load. I then removed the outer bearing and housing, removed the same amount of thickness from the shim stack as my end play and reassembled, checking the bearing preload with the rotational torque require to spin the pinion. I then adjusted as required...which in my case involved a lathe since I didn't have the combination of shims to hit the dimension I needed. This may have had something to do with me having the Daytona pinion support hard anodized, or it could have just been the shim kit I was given.
My differential used all new parts, including the case...and I can say it doesn't really matter where you start with respect to the pinion depth IMHO, it's just a guess. I've read so many conflicting suggestions online and in various resources, some said to start at .012 and others were in the mid to upper .020's. What I ended up doing was about 6 different setups all said and done, although I probably could have done it in 3-4 with what I know now. That said, I'd do one high, one low and one in the middle, as that should give you a good idea of what type of pattern you're going to be looking for. Based on the high and low patterns, you should be able to tell whether you need to go up or down from your middle choice. Different gears will give different acceptable patterns. My pinion housing shim thickness ended up being much thicker than I expected, but with an aftermarket case, pinion support and gears, not too surprising really.
With each pinion depth change, you'll need to reset the backlash accordingly and then check the pattern. You should get a feel for it pretty quick once you see the pattern extremes.
When it doubt, post up here and you should get some good input.
