the 05 999 has a heavier crank than the 999s from 04 and also no ti rods and milder cams

The bigger fairing on the 2005 bikes make them a better bet if you're lanky (like me), but the deals available on the '04 bikes are hard to ignore. Given your choices, I'd go for the 2004 'S'. But if you can find a bit more dosh, go for the 2005 'S' - no question.

That'll be quite a bit more dosh - around £3500 ;)