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The tolerances are tight because otherwise this could never be printed on the most accurate printers without the end result being sloppy. Try scaling the gears to 99%, but you will have to drill out the holes with a 5mm drill because they will of course shrink together with the rest. For the outer gear, 1mm extra could make it extremely sloppy, I wouldn't add more than 0.4mm. Given that it has a diameter of 100mm, this means you should scale it up to 100.4%.
If the end result still does not run perfectly smooth, pour some abrasive cleaner all over it, add a few drops of water, and spin it for several minutes. Don't overdo it, it will get even smoother after you have rinsed and dried it. The only disadvantage is that the lemony smell of the cleaner will stick to the model for months :)