T-45, Tremec, or T-56?

Was the T-45 only used until 1999 and then they switch to Tremec in 2000 for GT's? I guess I have a Tremec 5 speed in my 2000 GT? Is this a good tranny and how much torque can it safely handle? If not, what is the best tranny swap, I think T-56 would be a good bet but they are expensive. I'll be around 400 torque / hp when I am done with the engine mods.

TKO will do nicely, they're common and will easily handle that amount of torque. even a built t-5 will serve your purpose.

You could probably keep the stock TR-3650 in your car, I know people running about 500 horsepower with a stock T-45. A properly built TR-3650 should be more than enough for what you will be cranking out. Not to sound like an ass, but I don't think you have to step up to the TKO yet, you said you would be at around 400 lb/ft of torque and 400 HP, and the TKO is rated at 425 lb/ft of torque, the TKO II is rated at 475. The nice thing about the T-56 is the extra gear, but it's very tall (0.5).
If I'm not mistaken though, the T-56 in the 03 Cobra is rated at 450 lb/ft torque, and I know plenty of people that are way over that and have never had a problem with it, know 2 guys that are close to 600 lb/ft of torque with the T-56. So in my opinion it's overkill to go with the T-56 unless you really want the extra gear. Hope I've helped.

the tall low gear in the t-56 is great for a car with a huge rear end gear like a 4.10 or a 4.56. helps the motor rev lower on the freeway so you use less fuel on long trips.

The T45 was taken out of the mustang in the late 2001 GT model year, after the Bullitts and Cobras had them installed in their units. The T3650 is marginally better than a T45, which was supposed to be marginally better than a T5 (which is debateable at this point). Though the 3650 isn't a bad tranny, its not the best either. If you can, go with a Viper spec T56. With that nice .55 6th gear, you can careen the streets in 6th with some 4.10s and not worry so much about gas problems. Plus, the fact that their a close ratio transmission doesn't subtract from the coolness factor either.

Plus, how many GTs do you know running around with a 6 speed?