can I put the tail housing from a 2wd 5speed on a 4wd 5speed or will the ouput shaft have to be switched? Im pretty sure I remember roast beef having to swap output shafts on his, just though I would make sure.

also, do all V6 5speeds have the same gear ratios(2wd different from 4wd,3.0 different then 3.3)?

As fare as I know 2wd and 4wd housings will not swap.

Yes there are different ratios of the v6 trannys. They vary a little through the years.