Thanks for the input, all.
I don't have much confidence in the same dealer to flush the system correctly, make sure it's properly bled, etc. I've PM-ed FordCustomerService to see what they can do. Luckily in the Southern California region, there are at least a handful of other dealers to choose from.
At the moment, I've stopped driving the car and will pedal around in my bicycle until the system is flushed.
2012 SE 5-door 5M 203A + Sport Package
2013 SE 4-door DCT