I think kingford09 is talking about CARB exempt status. Are you saying that Mass. has adopted CARB standards (which are California air quality standards and I know several other states use them)? I live in CA and they are a pain. If Mass. does use CARB standards, then you can not legally use a tuner at all, nor any modification that has to do with air quality (CAI, CATs, etc.). In fact, these can void your warranty.
That said, it all depends on your Ford dealer who does your service (or warranty work). You can call them and ask if they install the wires, and if so, will that interfer with your warranty. As for the tuner and CAI, you can use them, but you will need to put your tune back to factory before bringing it in and exchange any item (like a CAI) before you bring it in. In other words, if your dealer says you can not use that part (tuner, CAI, wires, etc.), you must swap them out before any service.
All that make sense? Any of it?
__________________ 09 V6 Pony Convertible Daily Driver-- Have: FRPP X pipe true dual exhaust, Eibach Pro-Kit lowering springs, Steeda camber plates, Steeda strut brace, and some dress-up stuff Next: C&L intake Bamachips combo, 4.10 gears + LSD. | 
09 Mustang Ignition and Tuner 
