Alex,
The shims are there to space the diff within the chassis brackets centrally. Centrally being the crux, failure to get it central will result in vibrations being transmitted through the car. I recon its better to leave the prop in the car thereby doing away with the need to drain the Gbox, just push it forward slightly and tie it up out the way fit the diff then couple up the prop flange. Thats how I did mine. Don`t forget to replace the blue prop flange nuts and to loctite them on assembley
Rob.