Most of those type axles use shims to move both differential carrier and the pinion. This makes them difficult to set up without having some special tool for measuring pinion depth and such. You had to pull them apart, reshim then put them back together to effect a change. Its also a balancing act between setting backlash and getting a good wear pattern between the two gears.
This is a good article about them. Its for a non Ford application but still has value. They appear to be a lot like a Banjo set up.
http://www.public.asu.edu/~grover/willys/timken.html
It might not be a bad idea to contact Chuck at Chuck's Trucks even if your not interested in his 4.11:1 gear conversion. He knows these axles a lot better than most folks.