Just bought a stock 2006 base Mustang 4.0 with auto tranny. I'm not going to be doing turbos or superchargers any time soon. One thing I recall from back in the day is throwing on something that boosts intake without expanding the exhaust side probably won't help as much. Also, the whole tuning factor I don't know much about. But whatever is chosen, I wonder about its impact on the drive train ( tranny ). This automatic was rebuilt June of 2013 at 65k miles ( mileage today is 89k ) so hopefully some of the improvements were put in with it.
Why any auto tranny, if not abused and serviced properly, would have to be rebuilt at 65k miles is really curious. Our 2000 ranger has a 4.0L V6 with the original auto tranny now at 155k miles.

 

If you are just doing CAI, tune, exhaust, your transmission should be fine.