Have you been disconnecting the battery through all of this? More importantly, did this all start happening after having disconnected the battery?
There is a TSB out for these engines depending on whether the car is over or under 10k miles. In other words, some vehicles had this problem quick and it was covered.
The throttle body gets coated in crap (oil) coming from the PCV (?.)
When you disconnect the battery, the computer forgets it's learned settings. Has to re learn them. Every time I have to disconnect the battery, the car runs like crap for about a month. Only at stop signs though and usually after it's warmed up a bit.
I did wipe clean the throttle body blend door and surrounding area, this helped a lot.
Not sure if it's your problem, but everyone here is talking about the same fixes that never work if you read other posts. Basically, the blend door is not adjusting properly at low RPM until the computer learns to overcome the crud.
Some people install the air/oil separators in the pcv line to fix such issues.
I've installed a new pcv and have the gaskets so I can yank the throttle body and thoroughly clean it. There's actually a special coating on these TB units that's supposed to prevent this issue. Doesn't work to well and points to the fact that Ford new about the issue from the design stages. hmmmm...