It's not exactly the most permament of solutions because I'm planning on adding the leaded glass at a later time, so the insulated glass part is designed to come apart with a razor blade and some time. Though if I were doing it again, I'd go with a rubber gasket instead of the silicone caulk just because of the messy nature of the whole thing. Rubber double-pane insulating gaskets aren't exactly common unless you're a window company though. I might be able to rig up something with butyl weatherstripping and some rigid polyurethane that would work.
The window is a weird size, which is why I didn't order one: I'd have to have it custom made, and custom made insulated tempered glass windows are a bit on the spendy side. The window opening is 9 inches by 70 inches, which isn't a normally stocked size.
Someday I will be done with this beast, really.