How to Restore the Default Permissions in Sierra?
This is really quite easy.


Make a back up (Just in case, etc..)
Download and install Mac OS on to the volume using a recovery HD / Internet Recovery or booted from a known good OS external (hold option key when booting)
Clean up user account permissions once the system is fixed.


Since all installs are archive and install, the operation to install Sierra drops a proper, SIP protected, proper permissions system and then calls Apple's migration scripts which should migrate all apps and configurations from the old system with proper permissions in place.

Then you can add a new admin user and remove each old user one by one - leaving their home folders alone. When you rename the old user home as a new short name - when you add those users in - that will fix the permissions on a per user basis.