I have a 99 Wrangler I bought used and have had problems buying the replacement windows. I bought some from Bestop that they said fits the factory top, which I believe is what I have but the zippers didn't match. The driver side window fit fine as the new window had the male stem end. But the new passenger side window has a zipper instead of the male stem and the top has the zipper and needs the stem part, so it will not go on. Hope that makes sense. The back window also fit fine, it was just the passanger window that wouldn't fit.
Thanks for any help!