+1 to the idea of tossing the sand. It's really not worth it to try and keep IMO.
As for storing the rock, I'd look in to ways of stripping rock like a bleach and muriatic acid treatment. After a process like that there wouldn't be anything left on it to smell, and you could just let it dry and store it in a box. You'd get the added benefit of that rock being good to go and free of organic material that could rot when you decide to set the tank back up again.
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