Here's a good page about the movie and the cars, including a link at the bottom regarding the whereabouts of the surviving Bullit Mustang. Most of the mods to the Mustangs used in the film were in the nature of reinforcements to the front unibody structure and specifically the shock towers to keep the car from bending in half during the landings when it went airborne in the chase scene.
Exhaust was glass-pack mufflers of the day. "Balchowski also had to do some tuning to the Mustang's 390ci High Performance engine to help it keep up with the Dodge's 440ci Magnum. Apparently, according to reliable sources, the stock Dodge would run away and hide from the Mustang."
Enjoy:
http://www.ponysite.de/bullitf.htm