Hi jkedge09.
My issue ended up being with my transfer case, not my transmission. Unfortunately, like you, my warranty ran out a short time before the problem started.
Therefore, Ford and my dealership did not have any obligation to help me. However, we did work out a deal with my dealership. Essentially I paid for the labor to replace my transfer case and the dealership covered the parts.
Of course I hoped for something more, but once the warranty ends, it ends. I learned my lesson on this one.
Good luck with your issue.