With 7800 hits on this thread there is still a lot of mistery about this issue.
When I came to the board some years back I saw the problem over and over with no answer to it.
Many want to blame the transmission but those days are long gone from when there was issues with the transmission that have been worked out by Ford.
Not that there can't be a trans issue but the hint is the way it shows up as a studder/missfire under specific conditions with no codes is the clue.
Good luck.