Flatiron,
Naj's photos don't really show the rubber gasket. But, his description is spot-on accurate on removal.
When replacing, my rubber was not reusable, and you do not want direct glass to metal contact here (or in most places for that matter...)
I found two materials that work well. The first is "craft foam" which you can buy in sheets (very cheap) at craft and art supply stores. It looks like colored paper but is actually thin foam. I think the thinnest stuff is about 1/16" (.0625") before any compression. The other was a roll of rubber. Have no idea where I found it, but probably at an auto parts store. Like a roll of electrical tape but it is rubber and made by 3M.
I also put a piece of this craft foam (which comes in plain and self stick varieties) on the bottom of my door. You see, due to the variabilities in window adjustment with the top(s) up, when my window was all the way down, one of the metal arms was just barely making contact with the bottom of the door. This made an unbelievable racket of noise (as if we need more noise in these cars...) when I was crusing, and hit some bumps with the window down. The foam on the bottom of the door provided a little cushion for the arm and the noise went away.
So, while you have your door open, and while you are adjusting everything, verify that the arms are NOT making contact with the bottom of the door with the window properly adjusted and all the way down. If you do have contact, add that foam.