Check this link for the differences from the 03 999 and 03 999S. Still the same address passed by Steve, just refined for the 03.
As I am still a track rookie, can not really help on setting the bike, but my two cents suggestion is to go in the track as it is and work your way forward in the setting of the bike after you understand how the bike beahave std. setting...
http://www.ducati.com/my2003/superbike.jhtml