There are many variations of both small-block (CSX2000-series) and big-block (CSX3000-series) Cobras, in terms of exhaust, etc. The 2000-series "street" cars generally had the so-called "undercar" exhaust system, i.e., pipes that ran underneath the car and exited under the rear valence. Check out my JCF in the photo gallery for illustrations.
Shelby also offered the "Nassau" exhaust on 2000-series cars. The pipes ran underneath the sides of the car and exited just ahead of the rear wheels. Similar to a sidepipe setup, except the pipes were still tucked underneath the car a bit, and didn't exit through the bodywork like the sidepipes on 3000-series cars. "FIA" and "USRRC" Cobras, as well as a very rare Shelby option called the "Slalom Snake" (set up for autocrossing, as the name implies) had this type of exhaust.
3000-series Cobras were also typically equipped with the undercar exhaust, similar in setup to the 289 "street" cars. 427 Competition and S/C models all had sidepipes, exiting through a rectangular hole in the bodywork just behind the front wheels. Some non-Comp/S/C cars also came equipped with sidepipes.
As far as body differences, some of the basics between the 2000- and 3000-series bodies are: the 2000s are narrower in the fender cross-section, the 2000s have a smaller grille "mouth" that is "D" shaped as opposed to ovoid, some 3000s have an
oil cooler scoop underneath the grille opening, 2000-series cars that were factory-equipped with rollbars have a forward brace, while 3000s have a rear brace (except for the first two or three factory comp cars, which have a 2000-style forward brace), 3000s have a different style shifter and different gauge layout (okay, so those aren't "body differences"), 3000s have their gas fillers on the passenger-side rear fender (as opposed to the center of the rear deck on 2000-series), 3000-series came with wider wheels from the factory, and the side exhausts, where installed, were different as noted above.
That's all I can think of in this sitting. I'm sure I left out a few hundred details, and I'm equally sure all of this is probably covered by ERA's website, which is excellent.
Bob