On my gearbox I pushed the slipper side bearing into the gearbox/motor mount making sure its fully seated then pushed the layshaft through with the metal shim and one plastic shim as per picture below:
I then did up all the bolts on the gearbox and checked the end float on the layshaft, it had a tiny amount of free play which is what your after as you don't want to add too many shims as this will bind up you gearbox.
The gearbox assembly:
Note: If you want to run the gear cover and use the rear motor Proline Losi 22 shell (As per Lee Martin) mount the gear cover using a long m3 bolt and nyloc through one of the fins on the motor mount.
This simply drops straight in the chassis and bolt the rear tower to the gearbox and job done!