Taking it to the Ford Dealer would be a fantastic thing to do, as your Ford dealer would tell you. My Ford dealer would have been happy to do the 30k service for $250, and somehow, somewhere in there, they figured in the coolant flush. What? Hello? I have the yellow coolant in there, thank you. That would have been $50 of the $250 total. Now I'm not saying all this to bash Ford, just the dealer. They were trying to squeeze every dollar they could to do unnecessary work. Sorry if I seem CHEAP

Notice the cheap cigarette.
Now on to your tranny question. Call around to other shops in your area. I called a local Midas shop and they quoted me roughly $100 for the 30k service. I asked them what all do they do for this service and they listed everything that I saw in my scheduled maintenance guide, so they seem to be pretty thorough. I just need to make sure they use the right tranny fluid and engine oil. They said they follow OEM specs. We'll see.
I don't know about changing the tranny fluid myself. Frankly, I don't feel confident enough to do it right, and I want to keep the warranty valid until the very end.