Our subject vehicle had been upgraded with an aftermarket clutch, flywheel, and numerous transmission mods, which probably add up to a G-note or two, which is about what you can sell the setup for used. Two-Valve owners wanting to upgrade are usually on the lookout for this type of deal, so keep that in mind.
Now that we've decided to automate this Mustang, here are a few things regarding the installation that you may want to make note of.
Our subject vehicle had been equipped with BBK long-tube headers. The passenger-side ball and socket flange was extremely close to the transmission pan, so the pan was slightly modified for clearance. We've also heard that the Kooks headers for the Cobra will fit the automatic too.
One of the key components in this install is the transmission harness, which is procured from any '96-up automatic Mustang GT. Unlike the GT and Mach 1s, the Cobra has no provision in the main harness to plug in the transmission harness, so the end must be repinned into the ECM. The transmission harness is made up of 12 wires that go through a grommet in the tunnel and directly to the PCM. Wire count may vary depending on what wires you reuse.
The '03-'04 Cobras use two intake air-temperature sensors. A primary sensor is located near the MAF, and the downstream sensor is located in the intake manifold. The Mach 1 computer that is used does not have the two-sensor application built into the processor, so the primary is disconnected and the downstream is wired into the primary pin.
Speaking of processors, the Mach 1 SYM2 processor is the computer of choice, as it's the fastest ECM before Ford changed to the '05-and-newer Spanish Oak processors.
The intercooler pump relay is controlled by the Cobra ECM through a ground circuit. Since the Mach processor has no provision for this, the intercooler relay is wired to a chassis ground and comes on at the turn of the ignition key. This isn't a big deal since many Cobra owners put the intercooler pump relay on a switch anyway.
Where there would normally be an Overdrive light on the dash in a factory-automatic Mustang, the Cobra has a shift light for the manual trans. HP simply removes the bulb in the dash; otherwise, it stays on all of the time.
While you're under the dash, you'll want to connect the Neutral safety switch on the clutch pedal to the transmission selector module on the auto transmission. This will ensure that the car starts in only Neutral or Park.
The transmission tunnels are also different between automatic and manual-equipped Mustangs. There is a plate welded to the top of the tunnel on the manual cars, and if you install the auto shifter inside the car, it will sit too high for the factory bezel to snap back in place. You can cut and reposition the plate, but HP remedies this in a much easier fashion by utilizing spacers and mounting the shifter from underneath the vehicle.
Lastly, a 111/42-inch longer driveshaft is required and needs to have a 4R75W yoke. You can reuse the Cobra flange at the other end. It does require a stepped U-joint to mate them, but you can get it from the local parts house, or any good drive-shaft shop should have it in stock and can install it when they make the driveshaft.
With all of the particulars out the of the way, we can tell you that car owner Smith had an ear-to-ear grin after his first test drive behind the automatic.
On the dyno, the peak numbers suffered, but we expected a slight decrease due to increased frictional losses. Baseline horsepower was 643 (735 on nitrous) and 572 lb-ft of torque (713 on squeeze). After the automatic installation, horsepower checked in at 584 and 630 on the sauce. Torque registered 527 lb-ft naturally aspirated and 612 on nitrous.

The swap starts by disconnecting...

The swap starts by disconnecting the battery and then removing the shifter.

Depending on what exhaust...

Depending on what exhaust you're using, you may not need this step. We had to remove our long-tube headers to get the new transmission in the tunnel, and HP prefers to drop the K-member to remove them. To do that, you'll need to disconnect the steering rack and the front lower control arms. Then, support the engine at the front while the transmission mount holds up the other end.

After the K-member is replaced,...

After the K-member is replaced, the T56 can come out. At 125 pounds, it's no lightweight and actually quite close in weight to the auto minus the converter.

Next up for removal are the...

Next up for removal are the bellhousing and the clutch. Once these are out, remove the pilot bearing/bushing from the crankshaft.

Remove the T56 transmission...

Remove the T56 transmission harness.

Time for the swap meet or...

Time for the swap meet or Internet classifieds. These are bolt-in swaps for Two-Valve owners.

While the transmission was...

While the transmission was out, we opted to install the LDC Chicago cooling mod. This handy setup allows the coolant flowing into the driver-side cylinder head to flow out the back and into the passenger-side head where it eventually exits into the heater core. Many Terminator owners believe the driver-side dead-end can result in excessive heat around cylinder No. 7, and this setup is designed to prevent that from happening.

The cooling mod is installed...

The cooling mod is installed into the freeze-plug area of the driver-side cylinder head. It's then connected using the supplied hose and fitting to the passenger-side head. Be careful not to damage the O-rings during installation.

Before you hoist the 4R75W...

Before you hoist the 4R75W into the trans tunnel, mount the gear-selector module and other sensors, along with the automatic harness. Once the harness is fed into the interior, you can modify it to fit the Mach 1 computer.

Transmission Jacks make this...

Transmission Jacks make this job much easier. You can find trans mounts for your floor jack too if you're doing this in your garage. After installing the shifter from the bottom, with the appropriate spacers, install the transmission.

The torque converter for...

The torque converter for this application is a lock-up unit that features an approximate stall speed of 3,200 rpm.

You'll need an automatic-transmission...

You'll need an automatic-transmission crossmember to mount this bad boy up in the tunnel. We found that the BBK long-tube headers fit well on the driver-side. The passenger-side header came in slight contact with the transmission pan, which was modified for clearance.