@wschaefer1: Did you update any other plugins at the same time as Wordfence? If .user.ini and .htaccess are restored, and the plugin is disabled, I don’t know how this could still be causing any issues. If you don’t mind posting a link to the site, I could try to take a look also.
@vaypers: You can replace the .htaccess file with the one that you downloaded during the setup file, and check also if you have a .user.ini or php.ini file in the site’s main folder. If you still have trouble and need more details, please make a new post using the form at the bottom of the Wordfence forum here. (The www.remarpro.com forum rules ask us to keep each person’s issues separate, and it also helps us keep track of open issues, so no one gets skipped in long posts.) Thanks!
-Matt R