If you've already hurt the T45 in your 4.6-powered SN-95, new ones are available from D&D Performance or you could have yours rebuilt. As for the TR-3650, they're not available from the aftermarket yet, but likely will be as soon as 2000-'02 Mustangs come off of warranty.
Tremec TR-3550/TKO
The Tremec TR-3550 is probably the most popular five-speed upgrade for those who need-or feel they need-something stronger still than the FRPP heavy-duty T5, also known as the "Z" trans. A spin-off of the Ford Top Loader four-speed, it has the same center-distance as the Top Loader. But it adds several goodies to the pie, with, of course, the overdriven Fifth gear being the biggest advantage. It also has an aluminum case, countershaft tapered roller bearings, caged needle bearings under First through Third gears, an internal shift rail, and a torque capacity rating of 350 lb-ft. In 1995, a revised 3550 came on the scene and it's known as the TKO. Its 360 lb-ft capacity rating is due to its larger input and output shaft sizes-the only difference between the two. The TR-3550 has a 10-spline input and a 28-spline output, while the TKO has a 26-spline input and a 31-spline output.
Although the TR-3550 is known to have a reputation for a notchier shift feel than a T5, it's usually minimized by proper break-in procedures, the right lubricant, and the use of an aftermarket shifter. Speaking of lubricant, the TR-3550's brass blocker rings, which require a 500-mile break-in period, necessitate the use of GM Synchromesh fluid and not Dexron III ATF, which would cause synchro failure. There are also other issues with the TR-3550 such as the requirement of a different bellhousing (the Tremec and T5 patterns are different) and an AOD crossmember in Fox-body cars since its rear mount is farther back than a T5. But if you decide to upgrade to one of these gearboxes, whomever you buy the trans from will be able to assist you with the required parts to ensure it's a bolt-in affair.
All Hail The Mighty T56
Although this is mainly a guide to five-speed transmissions for Mustangs, we'd be remiss to not touch on the T56 six-speed, which is now factory equipment in only the second-ever production (the first being the 2000 Cobra R) Mustang with a six-speed-the '03 supercharged SVT Cobra. The main drawbacks to a T56 are its weight (115 pounds) and the price (at least $2,700 to get one installed in a Mustang). It can be done, though, and two versions are available from D&D Performance. The aftermarket Ford unit is rated with a 440 lb-ft capacity and its bellhousing bolts up to a 5.0 or 351W small-block-D&D also offers one that works with 4.6 modular motors. For the last word in a bulletproof OEM-type transmission, look no further than the Dodge Viper-spec T56 that's rated to handle a whopping 550 lb-ft of torque. D&D Performance custom rebuilds brand new Viper T56s using unique D&D parts that, among other things, make them fit behind a 5.0 or 351W small-block. Clearly, this unit is more than enough for even the most radical street car. For the full scoop on all things T56, call D&D or visit the company's Web site.
Where Are These Transmissions Available?
Although many dealers offer T5 and Tremec transmissions, two popular sources for new units are Ford Racing Performance Parts and D&D Performance. To procure a used T5 (remember the '90 or newer ones are the best), Mustang Parts Specialties is a good source. The contact info for all three of these businesses is listed below. And check out all three company Web sites, too, as they provide a wealth of additional information.