It could be a good deal depending on what parts it needs and how much rust there is.
What you described is not unheard of with the 4x4 version of the FS5W71C. For some reason a countershaft bearing fails and then the housing breaks. There is a company in Florida that sells rebuilt ones for a pretty good deal, maybe even cheaper than a used one. I read bout a guy getting one for $595, that is a good deal, but I haven't checked firsthand. Here is a link to their site:
http://www.manual-transmission.com/
You probably have read about the oil fill plug being an inch too low on the 4x4 FS5W71C from the factory, so it is a good idea to overfill it through the shifter hole or by parking the truck on an incline and filling it through the plug. I chose to overfill it through the shifter hole, that way I know it isn't going to be too low because I can see the fluid rising up as I pour it in, and not just guessing whether or not I have it on a steep enough incline to get enough in.
4x4 D21's don't hold alignments very well, especially if you off-road it frequently, so get one of those lifetime guaranteed alignments if you can. Speaking of steering, the stock centerlink is wobbly by design and should be replaced with a Heim joint one such as a HooHaa. The stocker isn't necessarily going to fall apart, but if you are going to replace it, spend a little extra on the HooHaa. In addition to all of that, the ball joints also go out more if you off-road more, and even more if you crank the torsion bars, but that should be expected I guess.