FINALLY, My truck has come home.
SO in the end the truck ended up needing a new engine. I will post up the service order so people smarter then me can read it and see what the dealership actually said about it.
On top of having the engine done I had them check the tranny and drain and replace the fluid, new fuel filter and rear brakes were in need of being done and of course new oil filter/oil etc.
The rental car cost me $1100 and change for 21 days. I am hoping to get reimbursed at least a little from Ford for it but I don't know. Guess their standard rate is $28/day so even if they just gave me that it would be $588 which would be half and totally fair as far as I am concerned because part of my cost was that I paid for the extra insurance on the rental car and would not expect them to pick up that cost.
Engine is pretty, stock intake was re-installed for a variety of reasons so if anyone is looking for a Bansk intake for their truck I am going to post up in the classifieds with it.