Hi Doug, unless there is obvious need to relocate the shaft, re-using the exact same shims is the normal practice. Doing a disk brake swap (involving a different knuckle than the one that came from the factory) is the typical reason to need to measure using the SST for different shims. Bearings are made to tolerances in the 1/10,000" range so simply renewing the knuckle bearings is not a reason to have to measure for new shims.
The grey soup is pretty typical of a worn out inner axle seal ("Birfield seal"). A little bit of grooving is normally not a problem unless it is so deep that you can catch your fingernail on it. With the part time locking hubs, you really won't have anywhere near as much to deal with as an 80 that turns all the time.