I did my 4wd clutch yesterday.
Did it without removing the engine and it is a pig of a job.
It is possible to do it this way, but there isn't any real benefit over dropping the lot out. Time and effort are about the same, if not more.
There are a couple of locating dowels, but that's not what makes it hard to split the box from the engine/transfer case.
The output shaft runs right the way through the transfer case and is in effect three shafts, a long thin one inside a shorter wider one that's inside a stumpy fat one.
The removal can hang up on these and it does take a lot of pulling and jemmying to free them.
Same goes for getting the box back on, the short shaft lines up ok, but the middle shaft can hang up half way in, getting someone to rotate the prop shaft helps the splines line up.
Then it's a matter of more shoving, jemmying and jiggling until the studs are through enough to bolt up.