Update: Took it to Ford on Wednesday and they said they found nothing wrong. I took the service advisor on a ride and demonstrated the clunk for him.
Took it back today (Thursday) and they just called saying I need to replace the "lower control arm bushing" on the right front. Sold only in control arm assemblies. Five hour job. $738. WTF!!! I told him to put it back the way it was and I'd be up to get it.
I guess two phone calls are in order: 1) to the service manager to b*tch about the fact that they did the recall without telling me and also to b*tch about the fact that they performed free work that supposedly is going to cost me $700+. 2) To the Ford recall hotline on the recall letter. Anybody have that number handy?