@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.ads-software.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