As the title says, I've recently upgraded my sites to a newer release of Ubuntu, which includes the transition from Apache 2.2 to 2.4. Most of my sites that don't have highly customized .htaccess files are working, but the sites that I have running Drupal only want to show Internal Server Error. If I disable the .htaccess, the site loads fine, but obviously rewriting the url doesn't work. I'm not sure what's throwing it off, but the problem starts with the very first command of the .htaccess file:

<FilesMatch "\.(engine|inc|info|install|make|module|profile|test|po|sh|.*sql|theme|tpl(\.php)?|xtmpl|svn-base)$|^(code-style\.pl|Entries.*|Repository|Root|Tag|Template|all-wcprops|entries|format)$">
Order allow,deny
</FilesMatch>

I know my way around the command line well enough, but I don't work with linux servers every single day. I could use some help in determining what's throwing this off. I've gone through the steps listed at https://linode.com/docs/security/upgrading/updating-virtual-host-settings-from-apache-2-2-to-apache-2-4/, appending '.conf' to the configuration file and re-enabling the site, and adding <Directory /path/to/public/website/> Require all granted </Directory> to the VirtualHost directive. The /var/logs/apache2/error.log really only seems to show a warning about a deprecated PHP function: <b>Deprecated</b>: Directive 'register_long_arrays' is deprecated in PHP 5.3 and greater in <b>Unknown</b> on line <b>0</b><br />.

What should I try next?

Updated to add: Actually I looked in the site's specific error log, and I get this message:

<IfModule not allowed here, referer: http://www.mywebsitename.com

If that helps to narrow down the issue any more closely.

Look for the IfModule directive in your config or .htaccess files. This includes files in /etc/apache2/conf-enabled, /etc/apache2/mods-enabled, and /etc/apache2/sites-enabled.

What version of Apache? PHP? Drupal? Are using using mod_PHP or PHP-FPM?

Based on what you have here so far, Vance's suggestion is a good one.