We're not sure if this is...
We're not sure if this is a little-known fact, but '96-and-up Mustangs have a unique security system called the Passive Anti-Theft System (PATS), which can cause problems for DIY engine swappers who aren't familiar with it. PATS is comprised of a trunk-mounted transmitter and an ignition key with a coded chip (arrow) that all work together to protect the 'Stang. When you attempt to start the engine, the PATS transmitter sends out a radio frequency signal that's picked up by the transponder in the key. Once the key's coded chip is recognized, the transponder returns a unique RF signal to the PCM, giving the OK for the engine to start and run. Engines swapped from PATS-equipped 'Stangs have no hope unless the processor, coded key, and transponder package are part of the process, or the PATS system is disabled with a plug-in chip or flash tuner.
Unless you're using a carburetor on your swapped engine-which we'll assume is probably not the case for many enthusiasts reading this, especially those of you who go with a big-dog modular such as the 5.4s-the new engine setup is going to need some sort of management system to control the amount of air, fuel, and spark it needs to run properly.
There is a myriad of add-on and standalone tuning devices and software that will easily facilitate mild-or-wild swapped engines. A plug-in chip is probably the least expensive option and will best serve an EFI 351W that utilizes factory EEC-IV programming.
Handheld tuners such as SCT's XCalibrator 2 are probably second on the low-cost ladder, and they're perfect for dialing in the nonelaborate SN-95 and New Edge mod-motor swaps that retain EEC-V electronics. While '96-'98 processors can all be used and manipulated for proper functionality, the '98 Cobra coupes have a PCM that's preferred by many technicians who perform Cobra and 5.4 swaps. The Snake's "AOL2" box is return-style fuel system ready and apparently has larger, faster processing capacity and speed than other PCMs, which makes it receptive to tuning changes.
Editor Steve Turner initially selected a '98 Cobra's electronics system as the engine management gear for his Fox 500 project car ('88 T-top LX). Steve and Paul Svinicki of Paul's High Performance are now of the attitude that the hatchback 'Stang's transplanted Shelby GT 500 engine can be operated with all of the Shelby's factory electronics, including the drive-by-wire system, which will be cool if they're able to pull it off.
Standalone ECUs and wiring harnesses are typically applied to hardcore swap applications. FAST's XFI system, ACCEL's DFI, and the new eMS-Pro from Spectre Performance are all worth their cost, as they'll alleviate the issues that go hand in hand with using a factory processor, mass air sensor, and wiring.
 This PCM is EEC-V programming's...  This PCM is EEC-V programming's magic box for Four-Valve engine swaps. The '98 Cobra PCM is identified by its "AOL2" code. |  Handheld flash tuners, such...  Handheld flash tuners, such as this XCalibrator 2 unit by SCT, are used to shuttle custom tunes into the PCM and record data of the swapped engine's vital signs during the dyno- or street-tuning process. The XCalibrator 2 unit works in conjunction with SCT's Advantage III tuning software. |  Higher-end, standalone management...  Higher-end, standalone management systems, such as this XFI unit from FAST, are perfect for big-horsepower modular swaps. Standalone PCMs and wiring harnesses can be interfaced with a Mustang's OEM electronics via the appropriate relays, allowing a switch to factory engine management in the unlikely event of an emergency. |
An efficient exhaust system is critical to the overall performance of a swapped engine. Naturally, with the 351W procedure being the oldest, there are several good header options on the market from FRPP, BBK, Hooker Headers, and other exhaust manufacturers that provide excellent expulsion of spent gases and maximize the torque value of a stroker- or power adder-assisted Windsor.
The 4.6 and Navigator crowd is limited to 1 5/8-inch short-style headers or stock Cobra exhaust manifolds for a Fox application (which may require some modifying), but full-length and mid-length tubes are available from Hooker, Bassani, JBA, Kooks, and most of the major header manufacturers for Four-Valve '96-'04 'Stangs. The mid-length, 1.625-inch SN-95 headers can be finessed into a Cobra-swapped Fox provided the chassis is laser straight and an SN-95 K-member is part of the swap package.
 Hooker's swap headers (PN...  Hooker's swap headers (PN 6223) easily handle exhaust chores for a Fox 'Stang's new 351W. The tubes are 1 3/4 inches in diameter and merge into a sizeable 3-inch collector for efficient venting of exhaust gasses. |  Right now, FRPP's Shelby GT...  Right now, FRPP's Shelby GT 500 short-tube headers are as good as it gets from a Ford parts perspective. These tubes will work with a Navi-engine swap, but minor modifications may be necessary. |  Stock does rock. Installing...  Stock does rock. Installing an '03-'04 Cobra engine with stock exhaust manifolds quells some of the potential fitment drama that can be expected with Fox or '96-and-up swaps. |