It could also be the ****ty speakers they put in there. I thought it was something rattling in my 99 as well until I replaced they. Even when I didn't have the radio on they still did some weird rattling cause they were blown. Takes ten seconds to put new ones in. Havent had anything rattle in the door since then.
1999 V6 Mustang Dark Satin Green , SR CAI, BBK 65mm Throttle Body, Screaming Demon Coil Pack, SR Lowering Springs, Pioneer Stereo, 2 12' inch subs and 1600watt amp, Green Calipers,