Dave,
I already have the Cobb AP and I'm kinda on the fence on getting the short shift kit or the Mountune intake next. Since you have all of them, what would you do next if you were me?
The short shifter is great and feels good, it has nothing to do with the tune so this should be no issue.
If you want it, get it.
I have chosen the Mountune parts for a number of reasons.
They have been working closely with Ford for a number of years.
They have great engineering backing with Roush.
I do believe that they WILL work out the details with Ford and preserve all OEM warranties on the US cars as they have in the UK.
The air box does not change the mas air flow meter or sensor therefore it WILL pass a California Smog Check.
I like that it does draw air from outside the engine compartment and there is no additional noise.
I like the Mountune intercooler because in MY OPINION it will recover from heat soak faster.
I too have the Cobb AP and am very happy with the performance so far,
I am sure that soon Tune Maps will be available that bring all of these into play.
What you do with your car and money is of course, your choice, these are only MY OPINIONS,
Dave