Well, I guess I have been a little confused. I read over the postings again, and I think I am now reading that your mech is infact and Ford dealership. I don't know why I though he was with an independent shop.
All of the sensors/controls that you mentioned in your post are either read or controlled by the PCM . I guess if you trust your shop, a new PCM would be the way to go. It just drives me crazy to see someone pay a stealership $800 for a $380 part.
link to an F350 pcm but I can't believe the E550's are much different.
Powerstrokeshop.com