I had mine in a couple of weeks ago and they replaced everything that they replaced on your work order, and I was experiencing the same problems. I can report that as of today (as well as right after I left the dealership) the noise has returned and been the same grinding/rattling/whatever you want to call it in 1-2 and 2-3. Obviously this is the noise that is supposed to "go away" after 1000 miles or whenever the "green clutch" wears in, but I don't see that happening. So if my clutch was worn enough that they had to replace the clutches after 20,000 miles and it still makes the noise, won't they just be replacing another clutch at 40,000 miles?
This is the 10th time I've had it in for this issue, have already escalated to regional managers and all the other rigamarole that comes with that. Regional manager now ignores my calls and doesn't return them after I leave messages. I guess it's time for the formal complaint letter followed by a BBB lemon law complaint. It saddens me because I had such trust in Ford after driving my '96 Ranger for over 12 years with 0 issues. On this car they've had to replace the radio twice, the passenger window switch, and the clutches all before 22,000 miles.
What a disappointment.