Did you check in the lower trunk area, underneath the trunk floor cover, to see if something is rolling around in there? (Also check the glovebox and the frunk.)
When I was new to the Model S, my J1772 adapter would roll around and clunk against the side of the glovebox. Wrapping it up in a towel fixed that problem.
From your description, the likeliest explanation is a loose rolling object inside one of the car's storage spaces, but if you've looked in all those places and can't find the source of the rolling clunk, it may be time to ask a friend to ride with you to help pinpoint where the sound is coming from, or you can make an appointment at the service center. (I don't think I'd worry too much about the battery pack; it doesn't have any room to shift sideways.)