The cover is more than just a covering. Its other job is to provide the correct amount of pressure on the ball bearings that support the gearshafts. These bearings need to be pressed with the correct amount of force to keep them running smoothly and quietly.
This pressure is provided by ring-shaped shims that fit between the bearings and the rear cover. The goal here is to choose the right thickness for the shims, so that they press with the correct amount of force when the rear-cover bolts are tightened to the correct torque.
The first step to choosing the shim thickness is to calculate the clearance between the back wall of the gearbox and the rear cover. Here, I'm measuring the shoulder height of the rear wall with a depth micrometer.