Being a Mac newbie
This feels like file system corruption, and permissions "fixing" won't help.
But being a Unix old timer, here's what I would do.
1st, I'd look into the system log files. Check /var/log/*. Not sure if your version has a system.log or something else, but start looking through these. Maybe you'll be able to see some real error messages that will point you in the direction.
I would then hook the system up in target mode and attempt to copy your critical stuff using multiple tars at top level directories. That way if you get a hit on a bad error that triggers the abort, you can work around it.
Or, I'd use "cp -rvp" to move stuff to a different disk.
Bottom line, I'd not want to use that disk again until a new file system has been created on it.
