I think the 98's had the most power and were the fastest stock but don't quote me.
What type of riding do you plan to do?
Biggest problem with them are the water pumps and counterbalance bearings. Make sure both are in good shape.
I would go for a 99+. It gets you a newer chassis and better suspension set up. The 2000+'s had a wider front suspension. I think in 01 and 02 they had Flatslide carbs. Those are a big help on the thump pressure to prevent your thumb being sore.
This is my 99 that I custom built:
I have it geared, PSI pipes and a ripsaw track and she pulls like crazy. I got to say I'm pretty happy with the combo.