Well almost the same...
Well, for the most part all of the 4.0's are the same.
BUT... the 97 and up have a crank flange with 8 bolt holes rather than the 6 in the 96 and earlier. Which means that if you have the later model engine you need a flex plate or flywheel with the 8 holes. It should be easy to see if the engine is on a stand. Your 94 has 6 bolts.
Also the exhaust port shape was changed but the bolt holes are in the same location. So not a big deal.
I also believe that the cam shafts have different valve timing and lift for specific years- not a concern if you are swapping out the cam.
Also the combustion chamber and pistons are different, smaller combustion chamber on the later models. I believe the valve size is the same. I think this was on the 97's but it could be the 98's
Should be no problem with mounting the old manifold to the new engine, if you cant make the connections to the new intake. Someone posted that the old alum. intake was a bit better flowing than the new plastic- I have never seen the inside of one so I dont know.
So if the engine does have the 8 bolt crank flange you have something else to get, but everything else will bolt on to the basic engine assembly.