It's kind of interesting to have watched (read) as you've gone from encouraging the 'Ford believers' to wanting to smash things. That's not meant to be a disparaging remark, just interesting to have watched it occur in 30 days.
I have empathy for those that have issues. While I don't have transmission issues (yet), I am plagued with the clunk. I understand peoples' frustration with having spent their hard-earned money (mine is a nearly fully-loaded Ti) on a vehicle to have to be told that their issues are 'normal' or that they simply need to drive it more. After watching the video and then following the Lemon Law link..
On the positive side, be thankful that you appear to have a decent dealership. They seem to be at least attempting to get your vehicle fixed, and that is a lot more than many of us have gotten. Hopefully all will turn out well for you in the end.
FocusFest 2013: Best of Show
Gateway FFW: Show Class Outstanding
September '13 ROTM