The 03 top WILL fit on your 2000. I put a 2006 OEM soft top on a 2000. Fit's like a glove.
From 2003 on, the top clips are narrower. So, you can't put an older top (97-02) on an 03-06 without changing the head liner on the top too. Best Top sells TJ tops from 97-02 and 03-06 but you can still go new top to older jeep.
I don't know if the window zippers changed or not, but it doesn't affect how the top will fit or the function of the windows.