I shamelessly stole Mark's door design and had a local auto upholstery shop make snap-on windows. The setup works superbly, and if it rains I roll down the softtop, snap on the windows, and it's "no worries".

I followed Mark's idea of leaving a *bit* more of the door in place, low enough to lean out and see, but high enough to protect/contain the passengers. The sill is a bit higher than the seat cushion. I'd follow the top of your blue stripe.

I like 'em a lot. The only thing I would do differently is add a zipper to the soft windows for those warm but intermittent shower kinda days. Common in the Colorado high country.