Insanely clever and impressive.
Some possible improvements.
1. Replace the big heavy mirror with a pair of laser galvos. They're literally designed for this and will be much faster and more precise.
Example:
https://miyalaser.com/products/miya-40k-high-performance-las...
2. Increase the precision of the master clock. There's some time smearing along the beam. It's not that hard to make clocks with nanosecond resolution, and picosecond resolution is possible, although it's a bit of a project.
3. As others have said, time-averaging multiple runs would reduce the background noise.
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