If you are staying with your stock setup, I have found DBA rotors (4000's) and pagid pads (RS19 or 14) to be a good thing. Also like the endless pad (PC35).

Alternatively there is a raft of upgrades out there (later model brembos, AP, alcon) if your budgt supports it.

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Rotor of Fail
Ducati 998s
Ducati Streetfighter S
496 CI Injected Big Block. Carbon positive???