Ugh. This is often discussed every couple of months. I don't think there has been any concrete resolution. I got nowhere with Bestop or any of the major outlets when attempting to investigate this. Most anybody can tell you is there are different part #'s for 97-02 and 03-06 and therefore one will not work on the other. I question that, BUT I have read on here and several other sites that there are some minor alignment changes to the w/s angle, door drop, etc. Then again, I think a few folks on here can state otherwise, having used newer/older versions on their respective TJ's. Best bet is to get in touch with somebody at BT that actually has some technical info/knowledge.
Good luck and be sure to post up your findings.
04 Sahara, with a lift, some stuff, and a few things, on some 33's, blah, blah, blah.
A perpetual work in progress. Too much to list, not nearly enough to matter.
My RigRater Score: 387RRv1.0 with a BOA of 18.92 (and just how exactly is this going to help me over that big arse rock?)
Always do sober what you said you'd do drunk. That will teach you to keep your mouth shut.
~ Ernest Hemingway