One of the primary problems with doing a chopped top is finding a place who will do the glass for you. Almost everyone who does a first time chop NEVER thinks of this. The problem is even greater when it comes time to do the windsheild with safety glass.
I highly recommend finding a specialist to do this for you. You will not do it yourself without severely screwing it up. Get a professional. You can search the web or talk to local custom shops to see if they know anyone who can do it for you.