CAI's are quite beneficial to the 4.0's compared to 3.8's. Only buy a CAI that requires a tuner after install. Installing a CAI without the tune will net you nearly no gains, and may cause the car to run lean. Check out American Muscle, they have a bunch for the 05+.
2005-2009 Ford Mustang Cold Air Intakes, Mustang Intakes at AmericanMuscle.com - Free Shipping!
Also you can get dual exhaust that sounds pretty good for the v6. I say get duals since it is a mustang (all should have dual exhaust imo) and you will gain more out of having dual piping. A lot of people use Borla, FRPP, Pypes, JBA. Now I do think the 4.0's do end up sounding higher pitched than the 3.8's, but it's still better than stock. Just don't buy an x-pipe, that'll minimize raspiness and the higher tone.
2005-2009 Ford Mustang Exhaust at AmericanMuscle.com - Free Shipping!
As with the CAI, you'll want to tune the car after you add exhaust too. It'll adjust the car's ECU and get the most out of the mods.
12 Black GT500 SVT PP l VMP TVS l JLT123 l O/R X l 28x11.50Rx15 M/T Street R's l BMR Suspension l Recaros
03 Sonic Blue 3.8 / 17 Magnetic Fusion Sport 2.7 EB