European 1999 bikes came to the USA in very late 1999, and were called 2000 bikes. They are actually 1999 Euro bikes, and were available in only 2 colors (a black/grey/silver combo and a rare Rossi blue/red combo). There was no 1999 Mille R, just the base model. These 1999 (2000USA) bikes came with rubber brake lines, red painted calipers, different heel guards, and were missing an external idle adjustment knob, and were also missing a front cylinder vacuum port used for synching the TB.
During the first part of 2000, the USA started getting real 2000 Euro bikes. We Americans called these bikes the 2000.5 model. This also when the Mille R was introduced. The base model came in 3 colors (gloss black, gloss yellow, and gloss red), while the Mille R only came in gloss black. These bikes had minor updates over the previous versions. The base models and the R models now came with gold-painted calipers, steel braided lines, a real idle adjust knob, and a vacuum port for the front cylinder. The throttle cables have also been re-routed. Bodywork (except paint), engine, and frame remained the same as the 1999 Euro version.
Then came the 2001 model year. The 2001 European model had significant changes to the bodywork, gas tank, headlights, frame geometry, brakes, dash panel, switches, and the engine. The motor was raised in the frame a few mm, and the head angle changed slightly. The gauges went to a orange backlight color. They started getting the new 4-pad Brembo brakes. The new engine featured bigger valves and a revised cam grind. The 2001 base model was available in flat black, gloss red, or a light blue color. The R was available in a flat black or gloss yellow color scheme. The USA 2001 bikes received all the major updates except the new engine. We got the 2000 engine in the 2001 frame and bodywork. All 2001 base model bikes did not come with a steering damper, only the R came with a steering damper (Ohlins).
Then came the 2002 model year. Same frame and bodywork (except paint) as the 2001 bikes, but the USA finally gets the updated "big valve" motor in the 2002 USA bikes. The base model is available in 3 colors (flat black, silver, and red), while the R came in flat black or gloss yellow.