had a similar issue...'05 4.4. I brought it in several times for transmission issue, always the same thing: jerky shifting on startup, and also the occasional 'lurch\clunk' that feels like getting rear ended.

Initially they did a reprogram..didnt work. They also couldnt reproduce any of what I was describing so it didnt go too far.

Just recently I brought it back again with the same complaint. They were finally able to reproduce something, so they opened a PUMA case. The end result of all that was that they agreed to replace the tranny under CPO warranty!