So my question is will the 4.0 motor out of a 1990 swap into a 1992 cherokee that had a 4.0? I know somewhere between there there was a difference in the motors, but i didn't know what it was and how difficult it would be to make it work with my 92. Thanks for your input.

 

You will have a problem with where the coil mounts to the block. They mounted it on the inner fender in 90 and on the bolt in 92. The 90 engine does not have the mounting bosses cast into it.

The question is really why would you? Can't you find another later motor?
The 90 is not an HO motor but the 92 is. Just about any motor from 91 to 98 should be a bolt in.