2005 model has the new top fairing - wider and without the vents. It also comes with the assymetric Termi system in a box and radially mounted Brembos. I think it has had a slight engine tweak too, but I could be wrong...
2005 999S also comes with the r version box swingarm. ohlins damper. ohlins front & rear suspension. 143bhp. Some kind of new lighter plastic fairings.
Sorry - misread the post! Yep, only the 2005 999S has Ohlins/radials/Termis.
2004 999S - Ohlins all round, non radial Brembo serie Oros. Mono or Bip in red or yellow. 136bhp (claimed)
2005 999 - Showa all round with Ti Nitrade forks, non radial Brembo serie Oros. Mono in red only. Bip in red or black. 140bhp (claimed). 999R swingarm.
To be honest, engines will be near enough identical spec.