As Dave said, there is no tuning or other mods necessary to get rid of the PAIR crap.
PAIR's purpose is to inject air in the exhaust stream under very specific circumstances to try and burn up any remaining fuel in the exhaust for emissions reasons. Getting rid of that feature will not cause any change in how the engine runs, though it might cause the exhaust to be slightly richer under certain circumstances, like at idle and on over-run. The vast majority of the time the PAIR solenoid is commanded closed by the ECU, so the bike runs like the PAIR wasn't there anyway. There is a possibility that the headers will run cooler and the cats will run hotter without PAIR since the cats will then have to burn off any unburned fuel that would have ignited in the header with the PAIR air injected.
The primary advantage of removal is elimination of the clutter under the tank for future maintenance. Side benefits are the small weight reduction, the increased airflow under the tank reducing heating of the fuel (more important for 1st gens), elimination of popping sound on deceleration especially for those with louder than normal exhausts (that's the sound of the unburned fuel igniting ahead of the cat).
