Problem with Aggregating Households Extension after upgrade to 5.3.1
Its not a good idea to add manually in CiviCRM module folder. The system should pick the file from custom php or extension. Looking initially at the debug you provided looks like the custom php path or extension path is not included. Here are few things i would try before making it work in a unusual way


Check directory path is set correctly.
Clean up CiviCRM caches
Uninstall/disbale and install/enable extension. (Note: If the extension is responsible to store data and uninstall would cause data loss than try disabling-enabling extension)
Check if existing extensions is conflicting any problem by disabling the extension and trying.