Depending upon the application,...
Depending upon the application, the D&D Performance T56 conversion kit ($2,999) will contain a new crossmember and adapter, a 31-spline yoke, and, of course, the transmission. You have the option of purchasing a complete driveshaft instead of shortening yours. We opted for just the required clutch disc since we'd recently installed an 11-inch D&D Super Heavy Duty clutch ($299) in the car.
Horse Sense:
The T56 found in the Dodge Viper is not a direct bolt-in, of course. The staff at D&D takes the stock Viper-spec trans that has a torque capacity of 550 lb-ft (which they say is a conservative number) and blueprints the internals to bring the trans up to the latest updates and to ensure everything is perfect. Then they mate the T56 to a custom bellhousing, allowing a direct bolt-in behind a 4.6 mod motor (or a 5.0), having to do nothing more than shortening the driveshaft and relocating the transmission crossmember.
Back in the early performance heyday of the 5.0 Mustang, the factory T5 five-speed transmission was usually able to cut the mustard. Even when a supercharger was installed, the T5, often rebuilt with better internals, would last behind these performance upgrades. But as times changed and more people found ways to make power, the T5 became easier to break-a stroker engine and gobs of torque going through a grippy clutch usually spelled doom for the T5.
The boys at TTC (Tremec Transmissions back then) took an existing truck-based transmission and modified it to work with the 5.0 Mustang and offer up even more torque capacity. But in a few years the aftermarket would manufacture enough power to make even the Tremec TKO or TKO II wince at the thought of being bolted up behind 600 or more lb-ft of torque.
Tremec then offered the T56 six-speed in several GM platforms and eventually the Dodge Viper. Unfortunately, there was no easy way to get this stout transmission and its much-sought-after extra Overdrive gear into a Mustang.
The shifter area is much easier...
The shifter area is much easier to access on '94-and-newer Mustangs. Grasp the edge of the shifter bezel and lift up to free its grip. Unscrew the shift knob and remove the knob and boot/bezel. Underneath this is the weather seal. Remove the four retaining bolts for the boot and slide the boot out of the way. If necessary, remove the shifter handle to prevent tearing the seal.
Eventually, Tremec came out with Ford T56 aftermarket applications. Even the '03 Cobra bangs gears in a T56. But these models are rated at roughly 450 lb-ft of torque. This is much more than the T5 (300), the T45 (325), or even the Tremec 3550 (350-425 lb-ft depending upon model). The only other bolt-in transmission rated higher is the Tremec 3550 TKO II at 475, but it has one less gear and Fifth is a higher 0.82 ratio versus the regular 0.68.
For those who need even more torque capacity, D&D Performance-long a group of wizards in the ways of the manual transmission and clutch-began working on retrofitting a Viper-based T56 into the Mustang. The Viper's higher rating of 550 lb-ft means more strength behind the high-end street cars putting out 700 or more horsepower. And, with the Viper T56 you not only get the coveted extra gear, but also Sixth gear is a low 0.50 ratio versus the Ford T56's 0.62. After taking apart a T56, D&D "blueprints" it with the latest upgrades, including a steel 3-4 shift fork, carbon-fiber blocker rings on all gears (except Reverse, which still has brass), and verifying clearances and other minor details to ensure strength. The folks at D&D tell us in the five years they've been selling the Viper-spec trans to owners with "certifiably crazy power levels," they've never had a report of breakage.
The Viper T56 package comes with everything to install the transmission into your Mustang (there are Viper packages for the 4.6 and 5.0, and regular T56s for the 5.0) and only requires minor modifications to the crossmember mounting, shortening the driveshaft (or buying a new one), and adding fluid. Some applications will require a clutch disc change and a new, longer, speedometer cable.
Read on as we tackle the swap from a five-speed in Editor Turner's '98 Cobra to a new Viper T56.

With the weather seal and...

With the weather seal and shifter handle out of the way, the actual transmission and the shifter assembly are now visible. Remove the bolts retaining the shifter assembly and break the silicone seal to remove the shifter. This allows for more working room under the car when trying to slide the transmission back for removal.

The exhaust system will need...

The exhaust system will need to be partly removed for clearance. Unbolt the after-cat assemblies from the H- or X-pipe. Remove the nuts retaining the H- or X-pipe to the manifolds/headers and pull the H-/X-pipe out of the way. Don't forget to disconnect the oxygen sensors.

The driveshaft will need to...

The driveshaft will need to come out to allow removal of the transmission. In addition, the shaft will need to be shortened or replaced for the conversion. To reduce the downtime for Editor Turner's Cobra, we opted for a direct-fit driveshaft from D&D. If you haven't drained the transmission fluid, you will lose some from the tailshaft area, so either first drain the transmission or have a plastic tailshaft shipping cap ready to seal the transmission upon shaft removal.

Since the crossmember is to...

Since the crossmember is to be replaced with the modified piece sent with the D&D T56 kit (for our applica-tion), there's no need to unbolt the crossmember from the trans mount. Simply back out the crossmember-to-framerail retaining bolts until the retaining nuts on the bolts are free. Leave the bolts in temporarily to support the rear of the transmission.

The Tremec 3550 bolts to a...

The Tremec 3550 bolts to a bellhousing similar to that of a T5 with four bolts. Remove the four bolts from the transmission in preparation for its removal.

With help from fellow Primedian...

With help from fellow Primedian Randy Bolig, the 3550 is lowered, disengaged from the clutch, and removed from the Mustang. Two people can easily do this job-even flat-backing-as long as the car is high enough. Disconnect the starter and clutch fork/cable before unbolting the housing cover from the engine. If you haven't already done so, disconnect the battery as well since the cable leading to the starter is always hot and you don't want to weld a wrench to the starter. Be mindful that the housing-to-block bolts differ in length, so note where they go as you remove them.