Okay, here is what I have and need to know if it will work. I have a 1991 Cherokee with a 4.0, 4 speed auto and the transfer that has 2, 4part,4 full and 4 low in it. It needs a motor due to bearing knock and the tranny is starting to slip, so my brother gave me his 4.0 out of a 2000 wrangler that had a 5speed stick and I also have a 1990 cherokee with what seems to be the same tranny and transfer case. Will this motor from the 2000 and the tranny/transfer from the '90 bolt up together and drop into my '91 without any problems using my accesories and intake/exhaust manifolds from the '91?  

No. Take the complete engine, wiring harness and computer from the 2000.

The 2000 4.0 is very different than the '91 with regard to the computer, associated sensors, and ignition (2000 has coil on plug and no distributor).

The 2000 computer will not control tha AW4. The older AW4s used a separate computer to control the tranny but that was only with the Renix control system and your '91 has the Chrysler ECM. But, you can use the AW4 controller, and associated wiring and sensors, from your '90.  

The more that I have thought about it, the more I think you could swap all the sensors, ignition components, manifolds and all the drive accessories.

The heads and intake manifolds are different, but I think it would work fine. The magnets on the flywheel for the crank sensor are the same. The 2000 cam has slightly more lift, both intake and exhaust, and a longer duration, but again I think would be fine.

So, ya. Just use the long block from the 2000. Long block meaning just the block and head. None of the externals.  

That is what I was hoping someone would say. I have just the long block from the 2000 (using all my accesories) and wanted to know if they (meaning everything including sensors) would bolt on. I would also have to use my intake and exhaust manifold because he took his for his project    thank you  

Do you have the front balancer from the 2000? It is preferable to keep the balancer and the flywheel with the engine. But you'll be changing the 2000 flywheel for the '91 flex plate for the auto anyway. So, hopefullly the balance is ok. Should be ok.  

yea the balance will be ok, they are both internal balanced engines.