My primary concern would be cleaning the channels and checking for rust in the (front and rear). If you're sure there is no rust then it's up to you. Also, it's pretty hard to change broken trim retaining clips with the glass in also (at least the rear). Again, it's really up to you how far you want to go. I wouldn't worry about the side glass unless you are sand or bead blasting as you will never get the stuff out of the tracks without removing the glass and cleaning them. Of course errant media could damage the glass. I had to replace my rear glass due to the sandblaster hitting the corner with sand!
