I'd recommend "swiss cheesing" the door, but to keep the window working, use a 1' wide nylon belt with a clip on the end, hook the web into a hole in the glass, use plexiglass if ya really want it light, and screw the clip for the belt in the right position to hold the window closed. Gets rid of about 25 lbs worth of regulator and stuff, and yer window still goes up and down.
I had a pic of this being done, but now I can't find it. The clip goes on the inside of the door about 2/3's of the way down from the top, and he had a lil hook thing on both sides to keep the belt from going lopsided. When the window is down, the clip also keeps the window from falling all the way down in the door. Neat setup, works great, and it's cheap.