i had previously sound deadened my doors with damplifier from second skin audio and it totally kills any vibration and makes a piece of metal sound solid. so i agree: if you havent done this, do it while the regulator is out. especially put a piece directly in back of your speakers if they are mounted in the door panel.
those window winder clips are kind of tricky but i really have found that using the towel trick works well. you just need a very thin towel. and in my experience, the clip gets caught on the towel so doesnt shoot across the room or anything.
that inner seal, i think, has more effect in some climates than in others. i am in sunny california so it might not make much difference if i didnt replace it, but if i were somewhere with a lot of cold, rain or snow, it might be a problem. yeah you might get some drafts through the door panel that you might not otherwise. the inside of the door could be more prone to rusting out. basically i just think its a good idea to replace it as it came from the factory, especially because, at least on mine, the adhesive was still tacky and it could be pressed right back into place.
i think if i ruined or lost mine i would probably try to order one from the dealership, esp if it were pre-cut properly.
one love
jah bill