I thought the "S" had the same engine as the 999 but with Ohlins and Marchesini. The "R" has the higher compression engine with Magnesium instead of alloy (except in the wheels) - and carbon fibre + Ohlins.
06 appears to be the same engine & gearing wise:
http://www.ducati.com/bikes/my2006/p...rison&x=43&y=1