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Insulate the downtube. That is the best thing you can do to keep the tube batteries warm. Store it inside.
Crazy idea. If it's really cold make a heating pad out of rice that fits the frame, heat in a microwave, put around the tube and use an elastic bandage to hold it in place next to the frame. You can make one to keep you warm as well!
I like the bandage and waste heat concepts. How about a neoprene insulator that is designed to transfer motor heat to the downtube?