To close out on this.... I did call Ford Customer Care. In the end... Ford offered a 50/50 split of the warranty repair cost ($10,800)... or the equivalent of a 60/40 split if it was customer pay costs ($9,000). Even with the extra steps of the dealer confirming the issue with Ford (had to tear down the trans and pull the CDF Drum), getting cost/offer approvals, etc... it took only 2 weeks once my car was dropped off from start to finish.
Ford is also re-imbursing me the 2 weeks rental on a Ford vehicle from Avis (Note, they said Avis was covered @ $40/day... other companies up to $60/day). I have a corporate rate with Avis, so I was able to make the $40/day limit work with my rental. They did say I needed to rent a Ford vehicle... in case you're wondering what hoops you may have to go through with the rental. No courtesy vehicles were available at the dealer... at least that's what they said.
I agree with the last posts about taking your car to the dealer and documenting the issues at first observation within warranty mileage. I wish I had done it more and/or more recently. It is somewhat my fault as I was aware an issue was brewing and of the general problem because of posts on this board... but waited until the trans. started slipping between shifts and hard shifting in the cold weather this fall, when I was just past the powertrain mileage.
While not happy about having to pay $5,400 for a new tranny at 63k miles.... I'm at least happy it wasn't the full $9k. Lesson learned... take it in early, buy the extended warranty on high priced vehicles, call Ford Customer Care and request they help cover costs of repairs...
Also... I may think twice (or 3 times) about getting another Ford... second car in a row with trans. issues (I had a '13 Focus as well, damn DCT)