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Great result! I think for 3D-prints the best is not required.
For a simple, inexpensive and repetitive design - PERFECT!

Those who wish to further increase the accuracy can try using a polished steel shaft and bronze bushings (for example, from old CD-rom or very old 3"5 floppy disk drives. In FDD, shafts about 2 mm in diameter and about 30 mm long were installed. In the later constructions of FDD, such shafts stopped using at all. In CD/DVD-ROM - shafts about 3,17...3.2 mm in diameter). But such a change will complicate the design and add details that are difficult to obtain. With the accuracy already achieved (0.002! GREATLY!) It looks meaningless.

Another way to improve the accuracy can be the addition of a comparator to the circuit, which will increase the accuracy of determining the moment the phototransistor operates. In the Internet you can find a lot of schemes on the model of "comparator for phototransistor" or "comparator for optocoupler". It is better to choose a circuit based on a high-speed amplifier with low-voltage (5V) power, and pay attention to the temperature range of its application (especially if you use high-temperature plastics in a heat chamber).

IMHO, the accuracy achieved (0.002) is ABSOLUTELY SUFFICIENT. Although "True 3D printing maniacs" can try out of sports interest ... :)