As requested - the fumes will most likely always be a problem w/ this truck. Diesel in itself has a distinct and somewhat offensive smell as the soot will penetrate and stick to anything.
A/C/Heater draws air from over driver side of truck cowl.
Ford, orginally intended the truck to have a passenger air compartment filter on the passenger side of cowl but has never completed update.
So regardless of the manual may read - there is no filter I've seen.
On the passenger side is an opening which has been covered with an allweather tape. If you want to seal out the outside air - remove and you will find an opening to where the filter was suppose to be located (wire grid).
Under the dash of the passenger side you will find a plastic cover under the glove box. Remove - and look to the right and will see the vacuum diaphram that opens and close the door to the outside intake.
You may want to work the a/c controls to make sure your looking at the correct diaphram. In max position the door will open, in all other positions it will close drawing air from outside the cab.
If you want the system to always recirculate just air in the cab, you should remove the screws to the diaphram and disconnect the arm not the vacuum hose as the air pump under the hood will always run and other controls may not function correctly.
Find a way to keep door in the closed position and fill the top with expanding foam - spray in through the opening where the filter was suppose to be located(outside).
Reassemble without arm on diaphram and viola.
No more pungent diesel burn off.
Took about 30 min. to complete - easy for mechanically gifted.
Not too hard for the others.
Best of luck and hope it helps!

John

 

I had this same problem and they found that there was a cracked exhaust pipe, although I am not sure which one, but it was replaced and the problem went away. The dealership told me that they have been fixing approximately 2 a week.