With the advent of the modular-powered Mustang in 1996, the top-loader T5 bowed out in favor of the T45, an end-loading gearbox that, early on (say '96 through '98), suffered from weak internal shift linkage, notably the forks and especially the Z-links. These problems were all but licked by 1999 (Don tells us there were no less than 104 engineering improvements made between 1996 and 1999), and the late-production T45s that remained in use until the '01 model year were fairly tough units.
In mid-2001 a switch was made from the T45 to the somewhat heavier and presumably stronger TTC 3650. Interestingly, Don suggests Ford's reason for the change was not so much due to strength issues, but because the 3650 has a fully synchronized Reverse gear. This was in response to complaints that T45-equipped Mustangs were sometimes (often?) difficult to get into Reverse. Not much is yet known about the eventual durability of the 3650, but, at this time, the only place to get parts for one is through your Ford dealer.
The first regular-production Mustang (outside the ultra-rare '00 R-model) to benefit from a six-speed is the '03 Cobra, with its strong and smooth T56. Versions of this admittedly pricey but oh-so-beefy box are now available to retrofit to virtually any pushrod or modular Mustang. D&D even offers a gorilla-tough variant originally engineered for the torque-rageous Dodge Viper. How tough is the Viper box? "In the 3 1/2 years we've been selling these," Don says, "we have yet to have a single gear failure." This has to be the ultimate manual transmission for any Mustang that sees more than just a quarter-mile.
And that's a wrap for now. Thanks for investing the time to read this not-so-brief overview of what your right hand and left foot command on a stick-shift 'Stang. Though we've no doubt raised more questions than we've answered, at least we have you thinking about what goes on beneath the floorboards every time you bang a gear. 5.0