The man I consider my mentor, Dan Fay, used to say that people in home shops frequently didn't give themselves credit for the tolerances they achieved in fitting parts. They might not be fitted to a *specific* dimension, but the one-off fit of, say, a piston to a bore in a home shop can be within a couple ten-thousandths. As long as you control both parts and you don't have to achieve "interchangable parts" tolerance, which implies specific dimensions, it's amazing what you can achieve in your basement.
As far as making something to a specific dimension goes, I think your +0.0004, -0.0000 is about as close as I'd want to worry about on a regular basis. Measured accuracy to under half a thou starts to get problematic.
Another story: years ago I took a night class at the local voc-ed school. The instructor was a machinist at MIT's Draper Labs. He regularly worked to a tenth or less, and said when an occasional job came along with a tolerance of a thousanth, it felt like he almost could do it with a hammer and cold chisel. It all depends on what you get used to....
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