I'm in the early stages of looking at buying a new 2004 999S and notice that the spec sheet for the 2005 999S indicates that:
"The motorcycle comes with a racing kit that includes a complete Termignoni exhaust system, an electronic control unit with race mapping and a carbon fibre silencer cover."
04 999 S v's 05, 05 has new swingarm ( approx £1100 ), new top fairing/screen (not sure on price but it should be possible to retro fit) comes with race exhaust but I think it steel version which can be bought for about £1000. Think 05 might have radial brakes as well. I've just been through this decision and went for 04 because the saving over a new 05 was so big ( £4000 ), I'd have been pushed to affiord 05 S but now have the bike and can upgrade if I have spare cash. Price I got it at would allow me to put 05 swingarm on and go part way to the fairing against a base spec 999 dealer price never mind an S.
Yep, 05 S has new swingarm, radial mounted brakes, bodywork made from new and less weight material, a small increase in HP (does it??), and the racing kit which means half (i think) Termignoni exhaust system, ECU and carbon fiber silencer cover. And, of course the new 05 front fairing and red frame. I think the 05 is a big overall improvment over the 04.
you can get a fairing upgrade kit for 03/04 bikes for the 05 fairings about £850 +vat as a ducati performance kit about £600 cheaper than individual items
swing arm £1100 exhast mod to make clear £150 Labour £200 approx cut down or replace belly pan to clear arm + repaint £200 ? Misculanious linkages etc £200