I've got about 6,000 miles on my SHO PP now and I've noticed that when I'm getting off the freeway and slowing on the off ramp my cars tranny 'clunks' a bit as it down shifts around 40 MPH or so. I just figured that although I spent alot of money on the car it's still a Taurus and that's just how the tranny is. I can't imagine anything is wrong with it.
When we purchased a 2007 Dodge Caravan new it made strange and hard shifting at certain times and that car was brand new too at the time. We took it to the dealer and they made some programming changes to the computer and it helped but was never as smooth as I thought it should have been. For that vehicle it only did the funny shifting when going from 1st to 2nd while driving slowly in store parking lots. Like it didn't know what gear to be in or something.
I've come to the conclusion that no matter how much I wish my cars had the 'perfect ride' they are still man made and will act 'funny' at times..