Realistically, any engine mod that allows more air to flow into it needs a tune for maximum benefit. The factory parameters will only adjust for so much. Comments above about a "cold air" intake are correct; the absolute best you can hope for is a few degrees above ambient temperature, and that's only while you're moving. This can be verified with an OBD scanner that will report the air intake temp from the PCM (I've done this many times). They will flow *more* air, not *cooler* air.
Because the engines are so similar, many upgrades for 1999-2004 Mustangs can be adapted to work. Trick Flow has a 70 and 75mm throttle body that will bolt on, and their intake kits can be made to work (though it's NOT easy). There are a lot of camshaft options available, and if you're willing to tear deep enough into the engine, porting and polishing the heads yields good results. Check out my Registry thread to see what I've done to mine (link in signature).