Recently had a similar experience. Replaced a set of coil-overs that had the left rear unit blow a seal and caused theoud bumping noise. I went back to stock setup, but the sound was just as bad and had more vibration from road noise. I replaced all 4 rear subframe bolts and torqued to spec...noise is gone!

Did you loosen rear subframe bolts to remove rear oem springs? I did, and replacing bolts fixed my issue.