There wasn't much difference between the CJ and YJ when it comes to hardtops - they are pretty much interchangeable. The TJ however had a different windshield angle from the YJ - I believe that the YJ had more of an angle or rake to it, while the TJ was more vertical.
I don't believe there is any adjustment in your windshield.
Put the hard uppers on and post some photos of what doesn't fit right. I'm guessing that the hard upper is hitting your windshield.