The theory here is probably perfect, ie fitting the windows to the hard top first. But just a point for those who don't have a refurbed soft top or whose soft top maybe slightly out of alignment, it probably makes most sense to set be windows to the top you plan to use most rather than stick to a rule that was for cars 50 years younger. I set mine to my hard top, and then nearly broke the windows when the soft top was up. My soft top has not been refurbed, and has the really annoying kink in the two arms that run along the top of the window. So for me, and maybe a few others, it makes more sense to fit the windows to the soft top, I think.
JH