Can you put one of those clear covers over the outside of the window well?
A caulk like Seal-n-Peal should work even with the cold and it would allow you to remove the caulk if you need to open the window at some point, do you see this being th case?
For my basement window I used the same shrink wrap type window insulation kit over the window to seal out drafts and add another layer of trapped air, but you have multiple layers of glass so sealing them each up is going to help alot.
I recommend taking the windows out and cleaning the glass before sealing them up as well, if you have to cover over the outside of the opening with foam or an old blanket or something so you can pull the window appart for an hour I think you will find it well worth it, that way once they are sealed and clean they will stay that way, letting more natural light in to your basement.
If you don't need the light in your basement then cut a tight fitting foam block to just block off the window all together.
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