The most notable difference is the cylinder head design. The 1999 engine uses a "high swirl" cylinder head, while the 1992 engine uses a "low swirl" cylinder head. The high swirl design improved fuel economy and emissions, but it also required changes to the intake manifold, fuel injectors, and exhaust manifold.
In addition, the 1999 engine uses a different crankshaft, connecting rods, and pistons than the 1992 engine. These changes were made to increase the engine's power and torque output.
As a result of these differences, it would be impossible to simply swap the 1999 engine into your 1992 Cherokee without making major modifications to the intake manifold, fuel injectors, exhaust manifold, crankshaft, connecting rods, and pistons.