El Capitan Installer consistently corrups HFS+ superblock
I would still suspect a problem with the superblock or GUID table.

Personally, I would copy the entire drive to an external drive then boot from the external and erase the internal drive. For this I usually use Carbon Copy Cloner

At that point you should be able to install El Capitan fine and then when asked by the installer you can transfer the applications, setting and users from the external drive into the new system.