I have an '03 with the Supertop. Have not installed it yet, I was missing the door surrounds. Just got those so I'll probably be pulling the hardtop and putting the soft on next weekend.
I believe the difference is the 97-02 used the factory mounts, and the 03-06 had a new type of frame. Instead of the attaching to the sides of the roll bar it has a bracket that bolts onto the top of the tub, in one of the holes the hardtop bolts use.
I could be wrong though, I didn't even know what I had until I researched it a bit, still not 100% sure it will work on mine. If nobody else has any solid info I'll post again once I try to put it on.