I've never changed the glass, but I installed new door weatherstripping on both doors. The little bit of advice I can give you from that is you can loosen a screw that runs through the metal channel that holds the weatherstrip in place which will allow you to pull it back a little (the metal channel), so you can move things around a little bit better.
Oh, and go slow. Getting the door panel, speaker, armrest, etc . and all that stuff off is easy. Fitting your hand into a confined speaker hole is not. I have a permanent scar on my left hand from the weatherstripping swap because the edges on the hole the speaker fits in are fairly sharp.