[pj7]

If they were both 100% original here's some differences -

02 will be 43mm WP forks or possibly the Ohlins option that year.
06 will be 45mm Marzocchi forks.
Both will have Ohlins shock but 06 has got a HS comp adjuster.
06 gets slightly smaller lighter cases as the counterbalancer cavity finally gets deleted.
02 frame is nickel plated, 06 is powercoated.
CDI has 2 maps built in on 06, difference between maps isn't much as I remember.
02 had 7/8" bar mounts standard, 06 was 1 1/8".
Swingarm pivot bolt was larger in 06.
Plastic will interchange but shape is updated on 06 (07 got the newer subframe, one piece tail plastic)
Fuel tank and seat are slightly different, 06 is a little easier to get forward on.
Frame is slightly different in motor mount location, steering head angle and bracing.

The two are close enough that most everything interchanges. In the end, for most people, a really nice 02 isn't really a step backwards from an 06.