UPDATE and final outcome:
After a couple phone calls to the dealer that bordered on irately angry (my wife, who technically owns the truck took the info from this thread and went after them like a maniac), no resolution and the dealer didn't really budge much from the original total $$ amount.
Then, we called the customer assistance number at Ford. An operator listened to us for a minute or two, then we were passed through to a customer care person who listened well, took a detailed report, was reasonably sympathetic, and kept us on hold while she called the servicing dealer to get their side of the story. We didn't get what we wanted in terms of a resolution (the service advisor and I disagreed about whether a transmission service was requested by me at the time of drop-off), but the customer care person was able to show us the warranty language online, and walked us through it carefully. Unbelievably, programming the Powertrain Control Module is NOT covered by the power train warranty - just about everything else is, though.
By that point, we're resigned to being ok paying for the transmission reprogramming and the oil change/tire rotation. We're still not ok with the transmission service and filter. So, we call up my childhood friend from up here and he drives us an hour to the dealership.
Finally a little luck at the dealership-- this dealer is owned by a family who have a summer home next door to my dad's. Two of the brothers have upper-level positions there, and I finally run into both of them on my way in the door. We catch up for a minute, and then one of them comes into the office with me and immediately eats the transmission service, due to the communication (estimate, repair order, and authorization) issues. We agree to pay for the synthetic oil change (he was going to eat half of that, too, but I'll just run a longer OCI this time) and the transmission programming. The labor rate in this shop is really low for a dealer, so the final total isn't all that bad.
I'm not happy, but I'm satisfied with the end result. I'm not one of those guys who likes to "pull rank" and cash in the "I know the owner" card, but in this case it's the only way this was going to be satisfactorily resolved without getting a lot of other people involved, and a lot more of our time. It's amazing how one weak link in the chain can ruin an entire dealer experience.
The truck drives and shifts well - even better than before, save for a couple of dirty clothes stains on the driver's seat… THANK YOU ALL for your suggestions and input - I'm better equipped to handle the dealer experience next time, for sure. (Until then, back to doing all my own service/maintenance whenever possible!)
