Be aware of the 0331 head issue (known to crack if overheated). Look for any signs of a crack (coolant in oil or vice versa, "Bars Leaks" or any other block sealer in the rad, etc.), this applies to all 00-01 4.0L I6s not just Cherokees.
00-01 XJ Cherokees also have the Low-Pinion Dana 30 in the front verses the High-Pinion D30 in earlier years, but this isn't an issue unless you plan to put a lift on it (particularly one greater than 3").
On a side note on your profile, if you have a 1994 Cherokee it is an XJ not an FSJ. FSJ/SJ Cherokees are the pre-84 Cherokees that are a 2-door Wagoneer, 84-01 Cherokees are XJs.
Jeep Model designations:
XJ: 84-01 "Regular" (not Grand) Cherokees.
SJ/FSJ: "Full Sized Jeeps" Wagoneer (pre-84), Grand Wagoneer, Cherokee (pre-84), J-Series trucks
YJ: 86-95 Wrangler (1st gen)
TJ: 97-06 Wrangler (2nd gen)
JK: 07+ Wrangler (3rd gen)
ZJ: 93-98 Grand Cherokee (1st gen)
WJ: 99-04 Grand Cherokee (2nd gen)
WK: 05-10 Grand Cherokee (3rd gen)
WK2: 11+ Grand Cherokee (4th gen)
KJ: 02-07 Liberty (1st gen)
KK: 08-13 Liberty (2nd gen)
MJ: Comanche (an XJ Cherokee based pickup)
CJ: "Civilian Jeep" pre-wrangler "Jeep Jeeps".
KL: The "new" 2014 Cherokee (what an ugly thing that is, think Pontiac Aztec).