According to the Haynes manual, the 2000 R1 got improved in the new silencer and remapped ignition+EXUP-valve+carburettors which led to a 7.9 bhp increase. Haynes also says that service intervalls are improved from 6000 km to 10000 km.
(And ofcourse, the new bodywork, fuel tank, strengthened frame, improved gearbox, modified springs front+rear, lighter break components front+rear.)