Okay, cancel my last post. I have a new working hypothesis as to wear the 'clicking' noise is coming from. I believe (fingers crossed) it is from the component speaker box hitting against my hard wired radar detector which are installed behind my glove box. The noise was really difficult to pin point since I sit in the driver's seat and my girlfriend's response was always, "All cars make noise, calm down." I am just happy because this is a much easier fix than dynamating my doors (again).
As a side note, my windows do no rattle and sounds like your door panels may not be on properly. On my old Subaru there was a piece of plastic that held the door panel into place that right next to the door. I left that out one time when I was into my door panel and it caused my windows to rattle. I don't remember seeing one on these doors though.