How can we best protect a stained glass window? (48" x 18")

We installed new replacement windows this year, but have yet to make or order storm windows for over four sets of stained glass bay windows. One window is protected under a porch, the other three see direct sun and elements.

What we thought of doing is just ordering a double pane low E insulated glass window from a local manufacturer, WITHOUT a frame. We thought we could then mount it by cutting wooden framing strips, to directly seal it in. We would like to caulk it permanently.

Can that be done, or would we have a moisture or heat issue? Can new storms be sealed totally, or will they need weep holes? If weep holes are needed, can we just drill holes through the INTERIOR sash, so we can fully seal an exterior storm? Or does it need to be on the exterior frame? How many holes and how large if so?