I had a VERY persistant door rattle in my Mazda 3. I finally took off the door panel and started messing with all the attachment hardware. It turned out that backing out (about 1/2 turn) one of the bolts that held on the window hardware stopped it. I guess they tightened it so tight at the factory that it was CAUSING a rattle.
Not saying that's what's wrong with the Focus, but sometimes you have to take the door panel off, and beat on the door lightly with your fist (to simulate vibrations) in order to find the source of the noise, and then make the necessary adjustments. Don't be afraid to get creative, as long as your fix doesn't impede the inner-workings of the door & window.