That 800's been sitting in the garage?
1) Gas tank issues - they don't apply to the '05 800 do they? It's a steel tank, isn't it?
2) Mods - most of the most popular, cosmetic mods (e.g., lites, bling, etc.) will work on both bikes, except the 800 is a wet clutch so you'll save money on those mods
3) Riding - for 99% of your road riding (even spirited) the 800 will be fine. If you're into engine tech, check out Brad Black's website
http://bikeboy.org/performance.html where you can dig-down and get his reports on the two engines. I don't think the shock/forks on either bike are fully adjustable, but, should work fine if you're not much over 200 pounds fully geared up.
4) The first thing to wear out on bikes are the soft bits (rubber hoses, belts, suspension, etc), so the 800 is less likely to have that problem
5) Check the service paperwork. First service at 600 miles, then every 6,000 miles after that. You can download the Owner's Manual for the S2R here
http://www.ducati.com/services/maintenance/index.do ; the 2000 model year manual is not available, but the 2001 bike should be similar.
6) I'd rather have the Marchesini wheels (if they're truly an aftermarket upgrade) than the CF....what kind of CF exhaust is it? Termignoni is the overpriced standard upgrade; other popular brands from that period include Arrow, Leo Vince, SilMoto, Fast by Ferracci (I think rebadged Silmoto and, perhaps, Arrow); some of the newer options include Zard and MIVV. Brembo are the stock brakes and probably the stock wheels (not logo'd), so no added-value there.
7) Price for the 800 seems a bit high; I think that bike retailed for around $8.5K US when new (unless that is a $2,000 set of aftermarket wheels on the bike, but you shouldn't have to pay for their upgrades).
Good luck