I recently went and used tips highlihted in a previous post it seemed to work great except some of my plugins didn’t work. I did a bunch of digging and found that the htaccess was causing a problem. Read More Below...

What was happening was that it was blocking access to PHP files. NOT fun at all so I updated the htaccess in the SPECIFIC plugin folder to be.

<Files ~ ".(css|jpe?g|png|gif|js|JPE?G|php)$">
Allow from all
</Files>

And that solved the problem.  So if there is a problem with a plugin after hardening look in the logs for “client denied by server configuration:” and see what may be blocked.