Is anyone using the two element version of the Yamahiko? Are the phase issues a problem for you?
I don't think there is anyway to phase align the two sources in this scenario. I know there are a lot of devices that are meant to phase align two mics or a mic and a pickup but this is particularly tricky because the source of the sound is changing depending on what string you are playing. IE sometimes the G bridge foot is closer to the sound source and the E bridge foot is further away an d then the opposite is true when you are playing a note on the E string. Maybe just really hi pass filtering the G side and lo pass filter the E side would work? The Wilson pick-up gets around this by having a piezo per string and the piezo close to each string.
I don't think there is anyway to phase align the two sources in this scenario. I know there are a lot of devices that are meant to phase align two mics or a mic and a pickup but this is particularly tricky because the source of the sound is changing depending on what string you are playing. IE sometimes the G bridge foot is closer to the sound source and the E bridge foot is further away an d then the opposite is true when you are playing a note on the E string. Maybe just really hi pass filtering the G side and lo pass filter the E side would work? The Wilson pick-up gets around this by having a piezo per string and the piezo close to each string.