Do the tune up before you burn money on the COP's. And buy the boots aftermarket as they will have a new spring in the package, I got some BWD's from O'Reillys AP. They are cheaper than the dealer parts and just as good.
The V-10 has the older OBD-I emission compliance regulations attached to it so you may not get a CEL whenever there is a skip. I pulled a 10k camper 125 miles on 9 cyl's and never got the light. (2001 F-350)
I also have a 2006 F-350 dually, and it is also listed as 'heavy duty engine' also. I never get a CEL when I fuel with the engine running, but the mis-fire codes will turn on the light.
The V-10 is catagorized as a 'heavy duty' engine so the emissions compliance is much less than a F-150 or a car.