FYI on the twin shaft trannies - they end up being wider than the tranny tunnel, requiring a fair bit of sheet metal work to make a new doghouse, which may also cascade into redoing the seat platform.
BTW, when I put the single shaft Spicer 6855 (sourced from a 5ton) behind the 3208 in the old build, it *just* fit into the tranny tunnel. Of course, the shifter needed to be moved, but having the tranny tunnel just work was a huge bonus. As another point of reference, the 13 speed in the new vehicle required a total of 5 extra inches of clearance under the floor (accomplished with a taller frame and then spacer blocks). The killer is that because the deuce design simply positions the crankshaft so darn high, unless you use a tranny whose single countershaft is directly under it, you run out of room in the tranny doghouse.
Now, I realize that the 13 speed tranny would be truly a stretch to install in a stock deuce frame and cab, and I certainly don't feel that you would need a full 5" or more of sheetmetal surgery to install any given double c/s tranny - but nonetheless, any double c/s tranny will likely cause sheet metal woes.
Best,
Bob