The main difference in the hardtop from a CJ to a YJ is the way the tailgate closes (both the top and the Jeep). YJs have a swingaway tailgate, so you're supposed to close the hardtop back window, then close and lock the YJ tailgate. The CJ is the opposite - you close the Jeep tailgate (looks like a pickup tailgate), then close and lock the hardtop back window.
I had a YJ top on my 85 CJ and it worked fine. I had to kind of close both of them at the same time, and if I "locked" the CJ tailgate from the inside I'd have to fold the locks down from the inside before I could open the tailgate.