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I would go with some 4.56 gears to start with and then go from there. A programmer, exhaust, and intake are a good start in the bolt on department. Also electric fans will free up some ponies.
I respectfully disagree with loosing torque by taking off the cats. Dyno runs have shown that the hp and torque increases are large above 3000 RPM but not as great below 3000. The butt meter usually sees this a a loss in the low end.
Go read the Mustang message boards. They have 4.6L engines and are all about increasing horsepower and torque for the drag strip.
I've been on Mustang boards for years now and own an 04 GT. You WILL lose low end torque if you ditch the cats, but gain in upper mid range to high rpm's. Mustangs are light with higher overall gear ratios (much smaller diam tires) so the low end loss is actually desirable to help with excessive tire spin. You want just the opposite with trucks, low end grunt is most desirable to get the mass moving. Just cutting the cats out will hurt that low end torque and without some serious exhaust mods will not gain much in the upper rpms. The original poster needs all the low end he can get with his combo, plus higher gears and probably a loose converter would help too.
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