The answer is simple, the factory intake is already a true cold air intake, and flows more air than you engine needs. Unless you run some kind of forced induction, you are not going to see any gains by changing the intake. Since there is nothing to gain by changing it, it needs to be left alone.
Real performance upgrades? You can run a Quarterhorse tuner. It will let you change things in the settings, and that could give you performance gains. Only go that route if you are familiar with how tuning works. If you are not, but still want to try it, do lots of reading before buying anything.
Exhuast mods in moderation can give you gains. The stock cats are fine, the stock y-pipe is a good design, the stock catback, not so good, a high flow muffler and 2.25" pipe is a good upgrade. The stock manifolds are restrictive, so headers can help.
The real big restriction however is the head and valves. The exhaust vales are a little small, so two things you can do to overcome that. You can get a cam that give more lift and/or duration on the exhaust valves, or get larger exhaust valves and the machine work that is related. The results are very real. You will see a hp and torque gain across the entire powerband that will be most noticed in passing gear. Porting the head, specifically the exhaust port is going to give you a good result in compliment to the valve or cam. Don't do both the valves and cam unless you have a tuner. The cam you would look for would be a street cam that advertises mild gains.
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