One thought that came to my mind was the pawls in the rear hub. I noticed a small click in mine frequently as I start pedaling with the motor on. I don't notice it when doing pedal-only power. The pawls seem to feed that click and feel more through the right crank because that's where the drivetrain is. At first I thought perhaps it was the clutch mechanism in the BBSHD, but the more I checked everything like the crank arm and such, it seemed to come from the hub but transmits down the drivetrain to where it feels like it comes from the motor/cranks. In my case I'm just about positive that's where my clunk/click comes from.
Now, some of this may depend on the rear hub design that each of us have. Mine is a Shimano XT older style with 6-bolt disc rotor mounts. These have what can be described as a fair amount of "play" before engagement compared to some others. These older Shimano hubs are not alone in this. Lots of hubs have some engagement play in them. It's not something as noticeable when I'm doing the pedaling, but the motor brings it out more. Don't know if this is anyone else's issue, but it's something to check.
Now, some of this may depend on the rear hub design that each of us have. Mine is a Shimano XT older style with 6-bolt disc rotor mounts. These have what can be described as a fair amount of "play" before engagement compared to some others. These older Shimano hubs are not alone in this. Lots of hubs have some engagement play in them. It's not something as noticeable when I'm doing the pedaling, but the motor brings it out more. Don't know if this is anyone else's issue, but it's something to check.
Comment