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But how do you know where to point them?

Believe it or not: more lasers

At those levels of accuracy, I would expect the refractive index of the not-quite-empty space space in our solar system to prove problematic.

I wonder if orbiting outside of the ecliptic results in less stuff (even down to hydrogen) in a meaningful way.

There is no atmosphere for a space interferometer, which is one of the main technical considerations for optical comms from orbit.