Keep in mind the OP has the early 05-09 4.6 3v which unfortunately the stock airbox is actually pretty restrictive when compared with the 11-14 Coyote 5.0 4v.. However it's not so much the airbox design itself that's restrictive, but rather it's the smaller stock 80mm MAF housing size which causes the restriction.. Although I do agree that with the right tuning the stock airbox is capable of producing up to 20 additional HP, the 4.6 3v motors never the less do benefit from both a tune and CAI combo..
If the OP is considering a CAI.. Just make certain that it has a full shield to prevent hot air from entering the intake manifold.. I would recommend Airaid as the top choice followed by Steeda, as both include full air dam shielding and also offer a non-tune insert that's removable for future upgrades that require custom tuning..