If you do this in the car you dont need to remove the output shaft or drivers side axle, but some people do and that is why I believe I mentioned a few variations on how to do it. Basically if you are doing it in the car it is easiest to leave the output shaft in the trans, then when you put the diff back in you will need to have one hand holding the drivers side cv/axle against the trans while tapping the diff over the snap ring on the output shaft with the other hand. The order of the shaft install doesnt really matter, as long as it is ready to be lined up with the diff once you have the diff gears lined up properly in the ring gear inside the trans.
