I think that the angular error is .057 degrees - not a lot! I was thinking of an exclusive or gate. If you feed this with two square waves, its output is the difference between them, i.e if they are co-incident there is no output, if they are 180 degrees out of phase there is a constant 5V DC. So with your figure there would be .057/180 X 5 = ~0 (.3 mV), not enough to get excited about. It could easily be swamped by what are normally considered as secondary effects, such as noise and switching transients.
Another technique could be a I and Q demodulator. This demodulates a phase shifted carrier into inphase and quadrature components. If you use your applied voltage as the demodulation reference carrier, then the I and Q channels will give you the inphase and quad components. If you phase invert the reference oscillator at a low frequency rate, then the I and Q channels should be the same amplitude but opposite in sign, so you can use any amplitude differences between the two phase to change the reference frequency's phase to null the out of phase component, the minimum value being the true one. Then the problem is that of accurately measuring the amplitudes.
Frank