I'm also having the exact same issues since I picked the car up in July of 2012 with only 199.7km. I've had both front control arms replaced which did help reduce the front noise but now I have been to my dealer on numerous occasions for the rear end noise which has also been happening since I picked her up. I eventually duplicated it with my dealer who said they can hear it and are not sure of the cause (which in turn I have told them its the sway bar links, ball joints and maybe even a shock) I have worked for numerous car dealerships(Jaguar, Land Rover, Mitsubishi and Volvo) and currently working at BMW I know very well what to expect from a dealer. They did try tightening down all of the rear and that only made it worse. I do get the rear quarter window glass cracking noise as well. Most frustrating thing is the ford service advisor that was making sure the dealer was looking after me ending up quitting and now I get the run around. *No suspension mods* Only MPT 93 Tune & BBK intake which were installed at 12,000 km. I have the feeling I will have to purchase a set of Coilovers /caster camber plates, Pan Hard Bar, Lower control arm w/ relo brackets, and anti sway bar kit. just not willing to spend the money yet to just fix a problem.
I also purchased the Ford Extended Service Plan.