It seems to have appeared out of the blue. That's why I thought that it might be related to me pulling stuff (spare tire, etc.) out of the trunk well while doing the VPG, but that doesn't seem to be the case.
Suspension is bone stock. Had an alignment done about a month ago, when I had the thrust arm bushings done. The clunking started just a few days ago, for no obvious reason. I was under it today, while doing an oil change, and nothing really appeared out of sorts.
Could it be something in the drive line, flex discs? slip yoke? I don't think it's transmission related, but I have been wrong before.