So it's been a week since I took my car to the dealer and it is acting up again with the same issue after they did a reset and update to the computer so I will be taking it in again this weekend. I will say though after the update my car has been shifting a lot smoother now.
So unfortunately I just started encountering this issue last week. I took it to ford today and they did a full reset and updated the computer. Fingers crossed I do not get the rough idle again. To be honest I am not very hopefully this fixed it now that I have read the posts from this thread...