All upper door,soft doors, and tube doors are compatible between 97-06. I believe only the rubber seal is different.
http://www.4wd.com/productdetails.aspx?jeep-sid=1058&plID=10735&partID=7188
"In 1997 they used a grommet style that clipped into the doors. Half way through 1997 they superceded into 1998 using a slide style attachment on the seals. In all of 1998 they used slide style attachment and in 1999 (to current) they switched back to the grommet style."