The biggest difference is in the trailing arms themselves and there placement.
The 99 has outboard trailing arms that you would normaly find. Where the 2000 has trailing arms that are mounted in behind the bellypan. Polaris only did this for the 2000 model year as they got too much flack from their dealers regarding the maintenance headache this created compared to the outboard design. They went back to the traditional style for 2001.
99 was kinda the half and half of the gen 2 and wedge, the 99 had a seat and tank style like the gen 2 but with a weird tail lite that raped arounf the back of the seat a bit, but if i rember right the 99 bulk head was the same as the wedge chasses just the differnt hood and tub set up