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All things being equal, and if you're willing to rework the entire exhaust system, you want to go with a Long Tube design. They will generally improve torque production in the RPM range where you drive most often.
If you want something that will connect to the stock exhaust, you're limited to equal-length shorties. I personally prefer headers to manifolds, but I don't know that the shorty headers really do anything for you performance wise, in most cases.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.