You really shouldn't need to change anything else. You may want to run a better flowing air filter setup to compliment the better flowing exhaust, but there's really nothing you can do with the computer. The computer uses the O2 readings to determine how much fuel is needed(when not at full throttle) so it should adjust as you drive it. I don't get any rattle with my exhaust so you need to check to see if any heat shielding is loose or if any nuts/bolts are loose. Worst case might be the insides of the converter being loose.