First off, most of the glass industry indicated the measurements of a glass panel by width x height. I will assume that since you said they were side lights the measurements are 9? x 46?. I try to ?see? what people are describing when responding to questions.
Anyway, if the new panel is a beveled piece, I?m not too sure I would worry about broken pieces. You would need to remove the panel to fix them anyway. That is easy with just a bit of prying and a bent knife, much like they sell at C.R.lawrence for removing windshields of cars. Here is a suggestion that many answer your questions. Put small pieces of the tape along the perimeter; say a 1? piece every 6?. Then make sure the top and bottom of the new panel are not touching the existing frame. A small piece of wood or lead or plastic or anything solid, blocking the window up would do. Add the additional molding as you mentioned but make a few small notches in the top and bottom molding so that you can create an air flow between the two panels. Just an idea.
Michael Mezalick
Mezalick Design Studio, LLC
www.mezalick.com