Hi Matt,
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it should in theory be easier to just use the phase-mod input of the NCO. Anyone have any ideas they would be willing to share?
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Your idea cannot work.
If you shift the phase of the NCO, then you shift the phase of the transmitted sine as well. So your dot-product of the NCO with the received signal will still be the same, as the NCO phase you added is in common to both paths.
You would need an NCO at the receive end if you wanted to align that NCO to your received signal. However, what would be the point? The measured phase tells you something about your propagation delay. It might be useful to you.
Note that this is what frequency response analyzers exploit; you inject a sinusoid into your device under test, and then measure the magnitude and phase of the output sine, and then use that to construct a Bode plot for the device response.
Cheers,
Dave