When a friend needed a rear window for his hard top, he simply took a huge sheet of wrapping paper, then outlined the shape of the edge of the hard top where the window sealed up against it.
He took the paper down to a Plexiglas shop.
They used that template to cut out a piece of Plexiglas for him.
He still had to drill the hinge holes, and he had to do some slight trimming to get it to fit properly. But, for around $100, it was a pretty good deal.
Plus, he asked the plexiglas people to use "tinted" plexiglas.
Once installed, it really looked good.
2003 Wrangler Sahara, 4.0L, Automatic, Stock, Full Metal Doors, Half Doors, Running 31x10.50x15s