I've done this swap a couple times now. The track widths are close enough, so go for it!
There was a slight difference in width between '80 and later and '79 and older, but the big thing there is that you need axles from '80 and newer becuase the front diff on these will be on the driver's side and the rear diff will be centered. There were some wide track FSJs in the '70s and the J-trucks were all wide. The '80 and up J-trucks are pretty rare, but these axles would be the ticket if you wanted to build a YJ that was wider than stock.
The vaccum disconnects were mostly in the early '80s, and they weren't in the long side tube like on a YJ or XJ. The vaccum disconnects were built into the diff on the driver's side. They are pretty easy to tell becuase the diff cover looks different from a regular Dana 44.
The front spring perches will need to be moved in by about 1/2" on each side. The passenger side is easy because you can cut off thee perch and reweld it. For the driver's side you'll need to weld the old spring centering pin hole shut (hint - drop a stub of a bolt in the hole and weld it to the casting rather than try to fill the entire hole with weld) and drill a new one, as well as do some grinding to make the U-bolts fit.
The rear is even easier, just move the spring perches.
The brake lines will all hook up. You'll want to go to the Wagoneer steering linkages. This means you'll need to put on a Wagoneer pitman arm and probably shorten the Wagoneer drag link. I'm usually working with high steer arms, so I don't know exactly how it will work if you are going spring under - except that it's easy to shorten the Wag steering pieces. The threads on the drag link are 7/8" fine thread, you can get a die from sears if you need cut it and re-thread. I've also gotten by with just cutting 1/2" from each part of the drag link and each end of the adjuster. If you go with high steer arms you'll need to shorten the tie rod too, same deal though, cut some off, grind it to size and use a 7/8" die to thread it.
If you aren't changing lift height, you'll normally need to shorten the rear drive shaft. Sometimes the front comes out pretty close, but usually it's a little off and ends up getting changed.
Let me know if you have any other questions about this swap.
You might want to check out this http://www.outdoorwire.com/4x4/jeep/projects/yjtransformation/ article too. It's a YJ with a Grand Wagoneer Dana 44 rear, and an F250 high pinion 44 front that was shortened to Grand Wagoneer width.
[ 19 January 2002: Message edited by: Nutter ]