Well, I finally had a chance to let them look at it again. Was not real pleased with the service manager who said Fords position on these kind of problems was basically if the door closes it is OK. Well after leaving it with them for a day it looks exactly like it did when I brought it in. They said they adjusted the upper hinge. Not sure how exactly you adjust one without adjusting the other? As a bonus they managed to swap paint with something white while they were working on it. Going to be contacting the service manager soon!