Exhaust System

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The stock exhaust system consists of streamlined cast iron exhaust manifolds, a 2.5" H-pipe with dual catalytic converters, and dual 2.5" over-axle pipes (OAPs) with axle-back mufflers. As factory exhaust systems go, this is fairly free-flowing. Indeed replacing the OAPs and axle-backs with aftermarket units produces no performance gain whatsoever, and most enthusiasts merely replace the axle-backs in the quest for a more aggressive soundtrack. The choke points of the exhaust system are actually in the front half i.e. the stock manifolds and H-pipe.
Merely replacing the H-pipe alone with a standard length off-road X-pipe produces an ~8.0rwhp/6.5rwtq gain, with ~6.5rwhp/2.5rwtq gained by deleting the cats and ~1.5rwhp/4.0lbft gained by replacing the H section with an X-shaped crossover.
The gains in HP/TQ achieved by replacing the stock exhaust manifolds with headers depends on their primary tube length and diameter. The peak-to-peak gains from 1-5/8" headers alone are ~9.0rwhp/11.0rwtq for the full-length and ~8.0rwhp/6.5rwtq for the 3/4 length, with the longer tube length really showing its superiority in the 2600-5300rpm mid-range. Full-length long tube headers combined with a shorty off-road X-pipe produce the biggest HP/TQ gains (~17rwhp/18rwtq peak-to-peak) but are illegal in some states and may fail emissions testing. They are also expensive to buy, expensive to install (unless you DIY), and require a revised ECU tune.
Mid-length shorty headers are a viable alternative that allow the retention of the stock H-pipe, or the fitment of an aftermarket mid-pipe with catalytic converters that are positioned in the same location as the stock units, thus allowing the vehicle to pass state inspections. While they have the disadvantages of being almost equally as complicated to install as long tube headers and produce much smaller gains in HP & TQ (~6.5rwhp/3.0rwtq peak-to-peak), they are also much less expensive to buy and don't require a revised ECU tune (a further cost saving).

JBA Replica Shorty Headers

Weight (pair) = 15.2lb
Collector length = 6"
Runner length no.1 = 14", no.2 = 10", no.3 = 18", no.4 = 17", no.5 = 15", no.6 = 11", no.7 = 21", no.8 = 18", average = 15.5"

These are advertised as shorty headers because they allow the retention of the stock midpipe, but are functionally mid-length with 10"-21" primary tubes of 1-5/8" external diameter. These are too short to produce any reflected pressure wave scavenging, especially from 2500-6000rpm where 1-5/8" diameter full-length long tube headers perform better, but nevertheless offer some improvement in exhaust gas flow. The biggest torque gain (6rwtq) is produced from 1300-2900rpm, right where the engine operates during normal street driving.

Pypes High Flow Cats

These 2.5" polished 304 stainless steel, 300-cell mini converters offer higher exhaust gas flow compared to the stock catalytic converters, but weigh only 2.5 lbs and measure only 11" end-to-end. Installed, they only take up 7" in length (considerably less than the stock cats), freeing up a lot of space in the undercarriage.

Ford Performance X-Pipe

The Ford Performance X-pipe was a standard fitting on the 2007 Shelby GT, and was the reason why it was rated 4hp/5lbft higher than the 2008 Mustang Bullitt. This cut n' clamp unit replaces the H section of the stock midpipe on the 2005-2010 Mustang GT. The result is improved exhaust gas scavenging, with torque gains of at least 4rwtq from 3900-5700rpm.