As far as I know ALL 999's,whether they are bips,S's or R's have the cold start lever.Pretty sure the Fila rep came with the sponsor stickers already fitted,..although I might be wrong.
The '03 bike came in red as standard,with the ltd edition Fila bike being added to the line up later.All 'R's come with a paddock stand,a numbered plaque and a 'race' exhaust.The '03 bike used a standard can with small outlets,...the later bikes got a full assymetric system with larger outlets.Full carbon fibre bodywork.
The '04 bike was an updated version of the '03 bike with new swingarm and it lost the light switch.(Lights now on all the time)
For '05 the motor alledgedly gained another 11bhp,....although that may be down to the way it was measured,rather than developed!
Bodywork changed,....new front fairing and now with a painted carbon guard.Seat unit now made of plastic.
'06 bike identical to '05,...although the Xerox rep was added later on.
For full details on all the models,check out Ducati's excellent website and their archives.
Ducati.com