I think the S engine has the deep sump for one (please correct me if I am wrong), possible different bore/stroke, cams, valves, compression.
Plus other stuff that springs to mind the S should come with an Ohlins rear shock and steering damper, the Bayliss/Bostrom variants of the S also come with Ohlins forks, and stand, cover, plaque etc, not performance enhancing, but additional to the standard S models