Crash, there weren't any major engine changes from 04-06. Power will be within 1-2hp (they might have changed little stuff like exhaust header and jetting I think).
I think it was '05 when they went to the 4th gen frame on the 450. Its not much different than the 3rd gen, in fact riding them back to back you probably couldn't tell the difference unless your a really advanced rider.
The suspension more or less got a little better each year - its got the same components all the way through but the valving and anti-stiction stuff got better as time went on (though if your re-doing it for SM this won't really matter).
The front forks on the '05+ have less offset (i.e. the front axle is closer to the bike) which gives the same effect as the 22mm tripples that everyone was using up to '05. Makes the bike turn better, esp on flat hard turns. I don't know how it changes its behavior as a supermoto.
If it were me I'd look for an 05+ but wouldn't pass up a great deal on an older model esp if it had all the popular mods:thumbup
No real bugs with any of them. They are all serious race bikes and require serious maintenence - oil changes every ride and valve checks every 5 hours are the norm, but hey you gotta expect some extra work when you have a 63lbs lump making 50hp:hail