From the ducatimonster.org FAQ (hold the flames!)
2001 upgrades and data:
• Available in four models: M900S, M900Metallic, M900Dark and M900Cromo. No 2001 Std ie.
• Increased diameter engine mounting bolts, new matching crankcases, new frame lugs, new oil pump and other engine internal upgrades.
2000 upgrades and data:
• Complete make over for 2000, after 6 years without substantial changes, include: EFI replaced carbs in 2000, HP increased to 78 (from 74), new hollow axle front forks upped to 43mm from 41mm diameter, full tach/speedo replaced the speedo cluster of 1994-1999, lighter wheels, Goldline Brembo upgrade, smoother 748 transmission, beautified rear fender and turn signals, new fuel tank with improved knee cutout area for taller riders. Retracting sidestand gone.
When they changed the tank they also change the shape of the seat, so you can't use the '00 tank on a pre '00 monster without changing the seat too. They also changed the "suicide stand" for a regular stand with an ignition cutout (that apparently doesn't let you warm the bike up idling in neutral in the sidestand) - the sidestand also grew a "ball on a stick" to kick it down (with which grounds out earlier than the old sidestand). Another change was to the handlebars - the inside of the ends changed so the old plastic bar end plugs don't fit the current bars 'cause the holes in the end are smaller.
S model on my 01 had alloy swingarm, 3 way adjustable Showa forks, and adjustable rear shock as well as previously mentioned rear calliper mount change for 01. S also got carbon fibre exhaust heat shield, side covers and front fender.
If you end up getting one I've got a set of Titanium Termi slip ons with DP ECU and open airbox lid sitting in the garage that I'm about to eBay once I get off my backside and take a few pics. If you or anyone else is interested....