Well first off, the back glass is tempered and can not be cut. So you would likely "sink" the glass into the package tray so it doesn't need to be cut. The side glass on that car I believe is all flat, and safety plate so you can just cut all new windows using templates given to the glass man.
The windshield is the biggie, can it be cut, sure. But it takes a VERY experianced glass man to do it. And expect a new window or two to be broken in the process (with no guarantee, so you pay).
It too can be "sunk", but honestly I don't like that option (front or rear). I would do anything before that. Cutting the glass is just one of the many things that sets the customizer appart from the "Craftsmen".
If you do cut it, you want to cut the glass before you get the top chop finished so you can modify the roof to fit the glass! This is one big mistake most make (I did myself on my first curved glass chop) you can't modify the shape of the glass, and cutting a section off not only changes it's height, it changes it's shape. So instead of chopping the top and then trying to fit the glass to the top, you cut the glass and make the top fit the glass.
I ended up making a fiberglass windshield using a windshield as a mould. I then cut the fiberglass windshield down to fit my chopped top. The fiberglass windshield was then used to modify the roof. The fiberglass windshield was then used as a pattern to cut the glass and wham, it all fit back together!
Brian