The car I got rid of for the 2012 Focus was actually a 2000 Civic, not sure when my Focus was built, but it was May or June sometime.
Anyway, as far as the transmission goes, it was a little clunky at first, but after I hit about 1000 miles it smoothed out a lot. The reason it took so long was because like you, I drive over 100 miles a day, and it's all highway, meaning the transmission doesn't shift as much, taking longer to smooth out.
MFT is fine with my car. It has choked up a few times, but nothing major at all, I feel one more light update will work all those clinks out. I think most of the problems from it occur when you try to change stuff to quickly, like going from screen to screen, stuff like that.
Overall it's a great car, I chose it over the 2012 Civic because I do find it nicer, and more comfortable, and more power too. As far as quality, Ford has been getting much better in recent years, while Honda has been dragging down a bit (though, it is still very good).