Known issue on the coupes. It's the regulator cable. Remove the vapor barrier, reach in and up. The cable running at the top is insulated by a 2-inch section of foam and a plastic clip that holds it to the door. Unfortunately the clip breaks, and the foam ride up the cable, creating a rattling sound that sounds like a loose pane of glass when the cable vibrates against the metal door frame.
If that's the sound you experience, that's the first place I'd look. When I did my door, the speaker housing can make noise, but that cable is the biggest offender. The speaker housing makes more of a creaking (as opposed to rattling) noise.