Here’s what I’d try:
1. Use CarbonCopyCloner to clone the contents of your internal drive to an external USB drive.
2. Boot from the external clone.
3. Re-initialize the internal drive.
4. Run Disk Utility’s “repair disk” feature on it. What kind of report do you get?
5. If you get an “ok” report, repeat the “repair disk” test FIVE TIMES in succession. Do you still get an ok report each time?
6. If so, “re-clone” the contents on the external backup BACK TO the internal drive…