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I was looking to make these, too - your designs look awesome. A couple thoughts -
-- if you make the slots for magnets into buckyball holders (IE sphere just a little smaller than max diameter) you could put auto-orienting magnets inside.
-- if you didn't have the embedded magnets, could (better said, SHOULD) you print as one piece? I was thinking of doing that upside down with the legs already added to the design, so that the entire thing would be a single print (with bridging for the (upsidedown) bottom of the component tray
-- could an exposed infill disk be used as an alternative to the cork coaster? that would keep it all 3d printed and if it were a separate print, could be a different color, even with a single extruder.

Thanks again for sharing these - they are fantastic and are on my "gotta print soon" list.