Yeah, the version with the bolt on shifter tower is the new style and more desireable because it uses the same trans-to-bell bolt pattern as the Dodge NV4500, so you can hybrid it to run behind a Cummins.
x2 on the Borg Warner t-case, if it has the PTO and a fixed yoke output that's what it is. I don't remember the number off the top of my head.
$1000 is a good price for tranny and t-case, especially for the newer style. I'd jump on it at that price . . . .