First you need to filter the fundamental and each harmonic to look at them individually.
Once you have each one, take the Hilbert Transform of each one.
Make a complex function of each using the original filtered signal as the real part and the Hilbert transformed one as the imaginary part. Then use another of the complex functions to get the phase. If you subtract each of the harmonics phase waveforms from the fundamental this should give you the phase of each harmonic relative to the fundamental.
I hope this is what you are asking for.
Randall Pursley
