I have the 1994 2wd with the 4.0 v6, and it's looking like im going to need to pull the engine. I have what appears to be an oil pan leak, and because of how it was designed the engine needs, at the very least, to be lifted. I figure I might as well pull it and do the rear seal and clutch at the same time. All of that to say, how difficult is pulling this engine going to be? I haven't pulled one, when I replaced my cylinder heads I left it in, so I'm not sure how big of a pain I'm looking at. Also I plan to leave the tranny with the truck instead of pulling it with the engine.

 

It's a manual by the way

 

Having pulled just the engine out in my 3 litre, it was difficult getting at the bell housing bolts.
Mating the trans up to the block was a real bear.
If I had to do it again, I would pull the whole thing if I had the room.

If you do decide to pull the engine with the trans, make sure the stick is in neutral before removing it.

 

Does the 3.0 have the bell housing as a separate piece from the trans or is it integrated?

 

It's all one piece (integrated), the bell housing does not separate from the trans.
On mine anyway.
I don't think that there were many options for the 5 speed manual. I'm not aware of any of the 5 speeds separating from that point.