The '01 has a rear disc brake, better front brake system, change in port timing that is much better than the '99, and came stock with the WP Shock.
Early '99's had the Paoli shock and rear drum brake.
We went from the '99 to the '01 this spring. We had a chance to pickup a relatively new '00. But after my son road both the '00 and the '01, he chose the '01.
We currently have two '01's for sale. Selling them in complete stock trim with new graphics still in bag/box. Have extra plastic, DEP pipe, bleedable fork caps, and triple clamps that can go separately.
If interested, simply email me and I can send you out a photo.