these are not shims they are basically big nuts as they are threaded
as long as you didnt disturbed the pinion you dont need to worry about gear pattern, drop the carrier into the housing, holding the bearing races on the bearings, (3rd should be pinion flange down like the pinion flange was bolted to the work bench)
now you will need to place these "nut/shims" on the outside of the beaings, you must make sure the mesh with the threads so that you can rotate them when you install the caps
follow the directions posted above to get them tight, .005 is what i always go for
btw, ive never used a dial indicator just a "feel" for the backlash