Answer:
The block is the same however there are some major changes to the ignition system.
The 1998 TJ 4.0L uses a distributor and an external coil mounted to the side of the block, where as the 2001 uses a cam position sensor and a coil rail that is mounted to the engine and attaches directly to the spark plugs.
I also believe that the A/C compressor is also relocated from the passenger side to the lower driver side of the belt pulley configuration.