Well... after some arguing with Ford, I got my car back yesterday. They found that the power window motor was loose, so they tightened it, and the noise went away... The other day, the shop foreman was arguing with me saying there was nothing wrong. Guess who was wrong, and who was right?!?!
They also replaced the struts for the trunk (which the shop foreman also said there was nothing wrong with, so I proved him wrong again) and the car is back in my loving hands.
The good thing that came from all of this is that the Service Manager at Apple Ford (Dwayne) and I now know who each other are. If I come back for other repairs, I'm going to talk to him directly and I know things will get done. He's the one that confirmed everything I was saying about the car in the first place.