I didn't think there was a difference in the forks themselves. I believe there was a change in fork seals beginning in 2006 when honda added a second seal. I believe that second seal is a two piece unit.
The machining in the lower fork leg is more on the 06 and above and requires another spacer there. The other difference is in the anti-dive cylinder. The factory changed the O-rings to a different material and changed the bleed screw from 10mm to an 8mm screw(or vice versa).
As James said the only real difference is the slider, left side was machined deeper to hold a secondary wiper for the fork seal. Other than that there is no difference, right fork sliders 01-10 are interchangeable, left fork sliders for 01-10 are also interchangeable except you need an 06 or newer seal assembly.