I believe you have to hook the Spartan 3 up via serial to a laptop and change the config in it to switch from 4.9 to ADV. I recently bought one of each from JRP (one for me and one for a friend) and they said to make sure not to mix them up.
The tiny rear diff is the same as an ae86 diff according to Amayama if I recall correctly, the transfer case on the other hand... that's basically made of chocolate