It takes 10,000s to move 3000km at 300m/s, so a synchronization error of 5ns in 10000s.Err no, it is 5ns in 60 ns because the clock desynchronization is off by 5ns.
CERN used clock transport to check a transit delay over a distance of 8.3km, and got a result of 40996+/-1 ns.
So the low velocity approximation would work fine for them.
So what's the problem?
Why are you still insisting on perfect accuracy?
Are you going to rework the analysis to include quantum effects and curved spacetime, or are you happy with the macroscopic flat spacetime approximation?
And there's an issue you haven't yet tackled in post 52.