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If you're clearing the codes, and it turns the light on again afterwards, then there's an issue still present. Are they the same codes you listed above?
So google turned up this on that 1639 code.
http://www.powerstroke.org/forum/6-4l-problems-forum/464370-p1639-fault-code.html#/forumsite/20554/topics/464370?page=1
Ford says theres a 39 drive cycle for those codes to clear... yes i run h&s thr tuner has nothing to do with the codes. I own the . Ford rotunda tool and ids software they cant clear it either