Perhaps I'm confused. You have a worn throwout bearing (which is quite normal, time for a new clutch) and you want to replace the tranny? What's the connection? What will that do for you that a new clutch (which you'll need to get anyway) won't do?
If you want to replace it, then yeah, unbolt the '98 4-bolt tranny and bolt in a 99+ 7-bolt tranny. 4 of the bolt holes match up, 3 don't - you just leave those 3 open. Well, there's also the matter of the starter motor, which will bolt on if you sink a bolt into the appropriate hole since the starter expects a stud on the tranny and new trannies use a stud from the engine. It's a very easy transfer, as far as tranny swaps go.
But I am still unsure why you'd do that if all you have is a worn clutch and bearings. Replace the clutch disk, the pressure plate, the pilot bearing, and the throwout bearing and be done with it.
Oh yeah, and re the center diff - no one really takes the trannies apart - just get a tranny that has a center diff still attached.