I eventually got it all to work 'in the lab' but nowhere near stable or accurate enough for a real life application. This was all done at very low radio frequencies with super low radiated power (under the license limits) and that of course complicated matters greatly.
The big game changer was to get hold of an atomic clock that I could run locally. That takes the sting out of synchronizing with external sources (such synchronization usually involves a PLL and while the long term stability is amazing over the short term it usually is quite terrible [1]) and using a relatively affordable SDR I was finally able to do this with enough precision to be able to differentiate between the ground conducted signal and the 'airwave' for one of the EU atomic clocks (DCF-77). It was really neat to see the effect of the day/night cycle on the propagation of the signal (exactly as predicted) as validation.