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Trial and error. Print a couple parts, test fit them, repeat until you have the quality you want! Different printers will behave differently - I always add an extra .15mm in some places on my designs, because that's the number that works best for my printer.

Generally, tolerances are only crucial when you have "ridges" in your pieces - for a no-frills 3x3 mechanism (like the one that will exist inside your Time Machine), you could get away with having no tolerances at all.