Thanks for the feedback so far. It's been really frustrating. To be fair the LBS has been working well with us to resolve, but someone there is going to have to ride it out for 4+ miles to isolate the sound.
We continue testing ourselves too. We've eliminated the PAS system, including switching back to the original front wheel, same results. I stayed off the seat, she stayed off the seat no change. I unclipped and pedaled with her unclipped, no change so it's not the cleats.
We spent time on the climbs where it gets louder. I pedal with her unclipped and it's bad, like a violin made out of barbed wire. I unclipped and she pedaled. Lower sound almost baritone and she is thinking rear hub. Could bearings breaking down fit the pattern of- miles to begin, most pronounced under pressure, no sound unless pedaling?