Have you had the door panel off yet to see what might be causing this? It's pretty simple:
- Remove screws from arm rest and door handle.
- Use a flat head screw driver and go around the outside of the panel and pop it off the door (they come off pretty easy)
- Lift panel up so it unhooks itself from the window area
- You will need to kind of twist the panel around to get the handle through the opening
- Don't forget to disconnect your electronics. If you can't get them by hand, then use some Needle Nose
You should be able to reach in and see if something has come loose. I had a lever come off a rail on our 94 Wagon, once it re-attached, the noise went away.