Permissions error after Update to 8.1.9

After updating to 8.1.9 I received a 500 error that stated it couldn’t access the web.config file (I’m using IIS 8). I fixed the permissions, then received a 401.3 error telling me the user does not have permissions. I checked and all permissions are fine. I did notice that there were no permissions of the “index.php” file. When adding my AppPool permission, I then get an error telling me either the site is down for maintenance or there is a programming error with the site.

I used “drush pm-update” to run the update. Not sure what my issue seems to be. Any ideas?

Drupal version: 


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