There're problems with increasing atom number. It is true that more atoms will allow one to resolve QPN easier, more atoms make clock rotations (along the Bloch sphere) much harder, as for a spin-squeezed clock doing Ramsey sequence, you need at least two pi/2 rotations to rotate the squeezed state.
Stupid question: what you're describing looks very similar to NMR (using RF to shape ensembles of magnetic spins, often shifting them around the bloch sphere).
You're right, the techniques in NMR like Rabi and Ramsey spectroscopy, spin echoes are all used in atomic clock experiments too.