The large 15.9mm diameter shims that come with the Mugen MBX5/R/T kits is only used between the 8x16mm bearings and the diff case to adjust the ring and pinion gear mesh. It is very rare that the diff has any slop in teh diff case that you would need a shim to take up this slop. The shims basically force the ring gear away or towards the pinion gear so that the mesh is smoother. On the old MBX5 and MBX5 ProSpec, most guys had to use two shims on the cup side to loosen up the mesh. On the MBX5T they typically don't need to be shimmed (at least all the kits I've seen and built). Please note that if you use double gaskets on your diffs, the ring gear gets pushed awy the thickness of the compressed extra gasket and the entire diff is that much wider too. I switched from one gasket to two gaskets and haven't used the shims since.
Best regards,