First, welcome to the club.
To start, depending on what type of hardtop you have, the rear glass section will either fit onto the rear door or the hardtop itself. The two side windows fit to the top of the roof section, and the glass bit you mention should fit over the front of the cab with the addition of a few pieces of rubber that you shold have had supplied with the hard top.
If you can post some pics of the hardtop, I will be able to give you more detailed instructions on how to fit it to the SJ. There are so many different types of hardtop, each with thier own methods of fitting them (although they are all pretty similar).
Different types are:
- * One piece with rear door glass fitted to top
* One piece with rear door glass fitted to rear door
* Two piece - solid rear section with rear door glass fitted to top
* Two piece - solid rear section with rear door glass fitted to rear door
* Two piece - multi piece with rear door glass fitted to rear door
* Two piece - multi piece with rear door glass fitted to rear door
* Two piece - multi piece with rear door glass fitted to rear door and glass cabin section
These are all made by multiple manufacturers who use different methods to fix them to the vehicle