You just re-use the same shims that were in there before. The new clutches will be thicker, but thats the idea, more force holding them apart for better traction.
For installing the ring and pinion you are supposed to have a pinion depth gage to properly setup, well, pinion depth
Most of the time, when using FMS gears, you can re-use the stock shims and you are right in range of pinion depth. Same thing goes for side shims most of the time.
You use a dial indicator on the teeth of the ring gear to check backlash, btw.
I've installed a few sets of FMS gears and all have been able to use the same size shims that were used in the factory. The ford motorsport gears are just that good. I'd never use any other brand.