Gotcha. Do you have a picture? It may be pretty obvious that it would or would not fit if you can post a picture. If we get that far I can do some measurements for you on my top to see if perhaps the factory glass would work.
I too have a 98 TJ with a Steelhorse hartop. My rear glass recently broke. No local glass shop will make it, liability issues related to it breaking from stress from the support struts on the glass is what all of them said. So I am in the process of cutting out a new rear glass from scratch resistant Lexan with a water jet this weekend I hope. I'll post the pictures after its done.
plexiglass did work but it's not a weather resistant option because of the flexing. While playing in a jeep junkyard i did find that the YJ factory hard top glass works in the tj steelhorse hard top dimensionally and the hinge holes line up. The only downside is that you will have to play with the steelhorse bottom plastic seal to make it fit with the door and there are no holes for the gas prop rods.