In 2003, we were blessed to finally get a T56 in a Mustang from the factory. This six-speed gearbox was considered bulletproof with its stout gearset and triple-cone synchronizers in First and Second gears. The 390-horse Cobra certainly needed this robust gearbox to handle all of its torque, but after a few track outings and dyno days, enthusiasts began to realize that even this ultimate Mustang still had some shortcomings in the driveline department. Over time, these issues have grown apparent and are now considered recurring problems on the '03 and '04 Cobras. Today, we will address the two most common-the clutch and the input shaft.
Built To Spec
The Cobra's factory 11-inch clutch has never been a model for long life, especially when slicks are part of the equation. It's also saddled with heavy pedal effort and vague action, making it almost unbearable for many to live with. Many Cobra owners relied on the aftermarket shortly after taking delivery of their cars, and the results were mixed, as finding the right combination of pedal effort, feel, and clamping power has been an elusive combination for a conventional single-disc design. However, with the advent of twin-disc technology being available to the Mustang masses (that would be you and I), we can finally get everything we want with an over-the-counter twin-disc clutch setup.
Although there are a few clutch companies out there that offer a twin-disc system for the 4.6L engine, few offer as many different versions as Spec. Its Super Twin clutch assemblies are constructed of billet aluminum and are a direct fit for any Cobra. They allow you to reuse the existing clutch release fork and require no machining or special fabrication. As a matter of fact, the assemblies are a direct replacement that replace your clutch and flywheel assembly in one fell swoop.

The first order of business...

The first order of business is to pull out the transmission and drain it. Yes, it's a gruesome task, and you'll probably make the Missus upset when you smell like old ATF, but buy her a pizza, and then go under there and get crackin'! Heave it onto your workbench or tool cart for easy access to the front cover-you want that stock input shaft out of there.

Using a 15mm socket, undo...

Using a 15mm socket, undo all of the front cover bolts and lay them aside. Using a flat screwdriver, reach into the recesses between the cover and the case and slowly pull away the cover. The cover is indexed with two dowel pins, so keep that in mind. Once removed, simply remove the input shaft.

Spec's Super Twin clutch assembly...

Spec's Super Twin clutch assembly uses two smaller discs to handle more power than a conventional clutch. The complete package comes with a billet-aluminum flywheel with a replaceable steel surface ring. The billet-steel floater disc rides within the billet-aluminum cover, providing surface area that's nearly twice as much as a single-disc clutch setup. Best of all, pedal effort is significantly less than stock. Owners of '03-'04 Cobras can certainly appreciate that.
For our test mule, we decided to go with Spec's most street-friendly setup, the SS-Trim (PN SF87SST), which uses one spring-hub disc and one solid-hub disc. Both use a combination of Kevlar and metallic facings for smooth engagement and, of course, massive torque-holding capacity. Speaking of torque capacity, Spec tells us that this SS-Trim can handle an incredible 900 lb-ft of torque without a whimper. For our Cobra, which currently belts out 453 rwtq (about 525 lb-ft at the crank), it won't be an issue.
Torque capacity is certainly great to have, but we also looked forward to taking advantage of the reduced pedal pressure. Because of the large amount of clutch surface area that a twin-disc clutch inherently has, there's less need for a radical spring rate, and this ultimately translates into a lighter pedal for a given torque load. This means we can finally cancel that knee replacement surgery!
Getting Shafted
The T56 is a darn-strong gearbox, but its weakest link is the 10-spline input shaft. When the folks at Tremec were tasked to fit the T56 into the Terminator, they equipped it with this 10-spline shaft to match up with the Ford clutch disc. Although it seemed like a good idea at the time, the problem was that in designing this piece, it was not as thick or robust as the 26-spline shaft that typically comes with a T56 when it is used in a Viper or Corvette. Of course, companies like G-Force Racing Transmissions can sell you the parts or build you a killer T56, but we went with this simple upgrade to keep down the cost.

Side by side, you can see...

Side by side, you can see how the stock 10-spline input shaft (left) often fails in the splined section. Its inner diameter is much smaller when compared to the 26-spline unit on the right. Where the disc sits is where these shafts often twist and break.

While you're in there, it's...

While you're in there, it's best to replace the input shaft seal. The old one simply pries out with a seal puller and the new one goes in the direction shown. We used the backside of a large socket and a hammer to install it.

When installing a new input...

When installing a new input shaft, you'll have to shim the mainshaft for the desired endplay of 0.000-0.002 inch. Simply assemble the front cover with the new input shaft, measure the endplay with a dial indicator, and add that number to the existing shim under the outer race of the input shaft bearing. We added 0.003 inch for zero endplay.
Side by side, we noticed that the thinnest part is within the splines where the inner diameter of the splined area is much smaller on the 10-spline unit. This is where many people have snapped shafts, even at lower power levels like ours (gee, who'da thunk that 453 rwhp would ever be considered a lower power level?). Going to a 26-spline input shaft is a highly recommended upgrade no matter how modified or unmodified your Cobra may be. We recommend having a qualified transmission shop swap the shaft for you, as getting into the inner workings of a transmission may be a bit daunting for the first-timer. If you're a hands-on kinda guy, it would be ideal to have a buddy that is familiar with T56s get involved, as he'll probably get dirty for a beer and a sandwich (much like us). Keep in mind that you'll need to order a clutch disc to match the 26-spline shaft.
With our Cobra put back together, we added four quarts of Royal Purple Synchromax synthetic transmission fluid and were rewarded with silky-smooth clutch action and tenacious bite. The best part of this upgrade was the increase in driveability and comfort. Pedal effort with the Spec Super Twin is literally half of what it used to be with the stock Cobra clutch. It makes the car a true pleasure to drive, and being stuck in traffic no longer makes us feel like we're training for a powerlifting championship.
Follow along as we swap out the clutch and input shaft in our own garage. With some free time and savvy wrench turning, you can also get some more bite from your Cobra's clutch.

With the transmission back...

With the transmission back together, we decided to mock up the new Spec clutch. Here, we slide on the two clutch discs and the floater plate to see how things fit. It's important to note that some aftermarket input shafts have splined sections that don't run the full length they're supposed to. That's bad because the forward disc in a twin-disc setup will have only a portion of its splines engaged onto the input shaft. To make sure you get the right one, ask whomever you buy your input shaft from if it has a full-length snout for use with a twin disc clutch. As you can see here, we have full and proper spline engagement.

With the new input shaft in...

With the new input shaft in place, we cleaned off the mounting flanges on the case and front cover, and applied a bead of silicone sealant. A cool thing to note is that Cobras come with a steel 3-4 shift fork from the factory, not aluminum like on some GM cars, which are prone to cracking. With the cover back on, we tightened the factory bolts to the factory-recommended 26 ft-lb.

Once back underneath, we removed...

Once back underneath, we removed the transmission wiring harness and unbolted the clutch housing with a 13mm socket and an assortment of swivels. The starter must also be undone, so don't forget to disconnect your battery.

The factory flywheel is aluminum...

The factory flywheel is aluminum with a nonreplaceable steel insert. With a 17mm socket, the eight factory flywheel bolts come right off. We then removed the pilot bearing from the crank and installed the new one that was provided with the clutch kit.

The Spec flywheel, also an...

The Spec flywheel, also an aluminum piece, bolts right into place. Positioning is critical, but luckily for all of us, the bolt-hole pattern will only line up with the crankshaft in one position. Reusing the stock steel bolt plate, we hold the flywheel in place with the proper tool and tighten the bolts to 60 ft-lb.

Adding some fresh grease onto...

Adding some fresh grease onto the clutch fork's pivot, we slid the included release bearing into place.

With the alignment tool in...

With the alignment tool in place, we slowly snugged the clutch cover bolts, making sure the installation tool would still glide smoothly in and out. The cover bolts were then torqued to a final 30 ft-lb.

With our tranny ready to go...

With our tranny ready to go back in, we took the advice of a friend and tried out his favorite shifter combination, which consists of a Pro-5.0 base with a Steeda Tri-Ax handle and shift knob. It turned out nice, giving the perfect combination of tight throws with ideal knob placement.

When all was said and done,...

When all was said and done, we filled the unit with four quarts of Royal Purple Synchromax manual transmission fluid, designed for manual transmissions that would normally use automatic transmission fluid (ATF).