MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Thanks Kevin and Joe! Putting the pieces on the table made me realize that I accidentally printed 6 of the small sides. I am printing the large ones now and will let you know how it goes!

Edit: I printed the correct sizes for the cube and that went together well. I had to print new larger pins for the gears at the bottom, and it's not perfect, but it works if I turn it slowly. Thanks for the help! :)