I haven't done a knuckle conversion yet, but if/when I do I will be using the tool to recenter the knuckles (since I now own it, but have it loaned out right now). But in your case it'd be easier to use the current shims like you said. My inner axle seals lasted about two years before they started leaking, and that was with a lot of wheeling, standard seals, and 0.012+ off to one side. I think you will be good for a few years.
Just pound the races in with a lead shot rubber mallet, using the tip Wes gave. With the studs you can tighten the lug nuts and it will suck the studs into place.