The 1995 Mustang Cobra R came with a 351 Windsor and a Tremec 3550 transmission. Edit: The 3550 is rated at 350 ft-lbs of torque but many people run them behind motors making more than that. I would recommend a TKO500 or 600 for a Cleveland, especially a 408 if you're putting sticky tires on the car or making trips to the strip.
http://en.wikipedia.org/wiki/Ford_Mustang_SVT_Cobra