There are a number of "difficult" problems with fitting fixed windows.
The top inner edge of the door, when extended forward to the windshield, falls
outside the windshield frame.
The front edge of the door falls several inches behind the windshield, so your window would have to extend past the door. (You could always have a fixed section, though)
If you change the upper door so that a window would actually fit, you will lose some very critical elbow room. Even if your fixed section (mentioned above) angled out, you're going to be very tight because the door slants in from the top, while the windshield slants out.
There's a reason that the original car used side curtains.