The rear liftgate is different on the CJ and YJ hardtops. A CJ liftgate closes on top of the CJ tailgate, while the YJ swingaway rear door closes on top of the hardtop liftgate. The CJ rear liftgate is a little shorter than the YJ liftgate, but I think if it interferes, you can cut off the YJ sealing lip and make it work on a CJ.
Also, they do make soft doors that fit with hardtops. Its theupper rear corner that is usually the problem. If it is a square corner that closes on top of the softop, its not gonna work with the hardtop. The soft doors that work with hardtos have a rounded corner, shaped like the hard doors.