How to remove output shaft

Axle or sometimes called output shafts go through tha actual bearing hub. You may have it confused with the transfer shaft. It comes out of the transfer box which goes to the differetial which the axle shafts come out of. The rear simply goes to the rear diff and its axles.
If you need to remove the other axle, just move the lower control arm and any other suspension such as torque rods that may make it hard to remove. Then get a pry bar or large screwdriver and pop it out of the differrential carfeully, not to much force, just a quick pop. Do not re-use the clips that retain the shafts.