You shouldn't need to change the depth of the pinion if you are only swapping to a posi carrier, so I would not suggest changing the pinion bearings. If you are doing it yourself, I would pull the pinion after you get the carrier out, and then look at the bearings for any pitting. If there isn't any pitting, then put the pinion back in and swap your carrier to the posi unit. Basically all you need to do is pull the carrier, press off the bearings from your open carrier and put them on your posi carrier. Make sure you take the shims off the open carrier and put them on the same side of the posi carrier befoe you press on the bearings. Put the posi carrier in, tighten down the bearing caps and check the gear pattern. It should be really close if not perfect. Yukon Gear and Axle has great setup instructions and specs on the net. Their instructions tell you what shims need to be adjusted depending on what your pattern looks like. Setting up gears isn't overly difficult, but it does take lots of work and patience.
Mark