If I remember correctly, there was a change in the water jacket openings/channels in the '00-01 heads resulting in a weakness in one or both ends causing those heads to crack, BUT I don't recall reading anything about whether or not the bolt patterns are different. Probably your best bet is to check out (if ur not doing it already) some of the Cherokee related forums, i.e.,
naxja.org/,
cherokeetalk.com/forum/f37/, etc... There are some serious Motor Heads on these sites
Sorry I couldn't help any more, but I'm not a Gear Head when it comes to the "real" Tech Info like this. Although...
(and this is just a guess) I would assume that any HO ('91-'01) Head should fit, of course, staying away from '00-'01's. You have to remember that pre-'91 is
not MPI. I guess you could ask a parts place to see if the head gaskets are the same for a '91 and '01, if so, then the bolt pattern is the same and water jacket openings would be pretty close.
Tatt