Have not done it yet, but my plans for this are as follows:

Remove the windows and cut out the entire side area to make a large opening. Then frame that in with either steel or aluminum angle to strengthen the cut out area. Then make a steel or aluminum frame to fill that area and glaze it in 1/4" Lexan. Ideally, I would like to have the window frame hinged at the top to allow folding the window up on top of the hard top for stowage. If the full hinge does not work, then use an easy to separate type of hinge to allow the windows to be removed from the sides and stored on top of the shell. Also would be nice to have a heavy duty screen over the opening for when the window is removed.