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^^^
I like the idea of a custom box too, but you still want the stone to be level. I don't mind my beautiful translucent amber base being under a killer stone in a lovely wooden box.
And it would...

Set it face down on a level surface, wrap it with tape, you want the tape wide enough to make the proper depth you want the base to be.
Run a light coat of Crisco, or something similar around the...