The stock exhaust manifolds are definitely restrictive on an NA set up because the runners are too small. The stock cats are also restrictive. Therefore upgrading the front half of the exhaust system with full-length headers will give you the biggest HP/TQ gains. Cat-backs and axle-backs are only for the sound.
On the intake side, the biggest restrictions are the stock air filter assembly and the charge motion control valves inside the intake manifold. Once you've done a CAI & deleted the CMCVs, the stock intake manifold with delete plates only becomes a restriction above 6200rpm. Therefore an aftermarket manifold would be a waste of money unless you're planning to rev the engine to at least 7000rpm. Even then, you'd need ported heads with upgraded valve springs plus longer duration cams to take full advantage of a manifold upgrade. Therefore the intake manifold should be the last item to tick off the list after ported heads & cams.
If you're going to remain NA my advice would be to do a JLT 3 CAI, Steeda underdrive pulleys (worth 8-10hp with no downside), DIY ported stock TB, DIY CMCV delete, full-length headers (if your state allows) or JBA shorty headers (if your state doesn't allow long tubes), a high-flow catted mid-pipe, and a remote e-mail tune (Lito is the best) with the rev limit set at 6500rpm. Collectively these are loosely termed "full bolt-ons". You could then do a DIY mild head port job, call it a day, and enjoy the fruits of your labor.
All performance cams will sacrifice torque below 4400rpm so unless you're going to spend a lot of time racing or want to brag to your buddies about the extra HP and the lopey exhaust note, don't bother. Ford already gave us excellent street cams with variable cam timing as the cherry on the cake.
if you have an '07-'09 GT with a stock 3.31 axle gear ratio, consider swapping in a 3.73 (for stock cams) or 4.10 ( for performance cams) ratio.
