Update to 7.59 after site hacked entity reference/ctools fatal error

Any assistance greatly appreciated. 

Site was taken down by host (Lonex) due to malicious content.  Attempting to scrub and update to 7.59 (late I know) and now receiving below updating error.

An AJAX HTTP error occurred. HTTP Result Code: 200 Debugging information follows. Path: http://www.my_site.com/update.php?op=selection&token=KvMsZy4zIh97UGrKqg5… StatusText: OK ResponseText: Fatal error: Call to undefined function ctools_include() in /home/www/my_site.com/sites/all/modules/contrib/entityreference/entityreference.module on line 194

line 194: ctools_include(‘plugins’);

I’ve downloaded and copied over fresh entityreference and ctools modules to no avail

Drupal version: 

Source: https://www.drupal.org/taxonomy/term/21/feed