We have installed several of the Pac Brakes on the 03 with 6-speed and no you cannot use the brake from the 01. The new brake is clamped into the down pipe using the factory clamp and replaces one of the elbows. One of the things we really like about the new Pac Brake is its integration with the PCM so you don't need to reset the cruise after using the brake, just hit resume.
As for the exhaust being 4", well sort of. It changes back and forth between 3. 5" and 4" several times.