If it has the original steel exhaust on it then check it for rust or any signs of welding to show that its been repaired before. The stock pipes are the best for the bike, but they just don't last and are getting a little rare now. Most people swap them out for stainless steel
Replacing the air filter with a K&N is a good way to go and replacing the rear brake caliper with the uprated thou caliper is a good mod but they are practically impossible to get hold of
Other than that, standard checks all round for signs of scratches, scuffs etc to see if its been down on its side. Depending on what year it is, it may have preload adjusters on the top of the forks (98/99 don't have these, 2000 on do
- if this doesn't match up then yours may have been replaced)