404 error codes and shibboleth issue

So I have a strange issue with a installation. this is a very large, very old install that I have taken over. I am trying to get it moved over and more streamlined but must maintain it until then. 

The following is the main setup versions

Rhel 6

Apache 2.2 (redhat default install)

Php 5.3.3

Drupal 7.x, latest as of this post to include drupalgeddon2 patch.

Under non ssl the site behaves 100% properly as far as I can tell, however under ssl the virtual directories drupal use (rewrite) server content but generate 404 error messages in the error log, in the chrome console, and anything like curl that pulls the site but not display it. 

To fix it you can set Allowoverride All, which is odd because that is the default setting for apache 2.2 and before it was not being set at all and the pages were serving. However once I do that  I get a 404 error message for shib. Again this makes some sense, due to all the rewriting done in the .htaccess file for drupal, but nothing I do makes this go away. I have added:

  RewriteCond %{REQUEST_URI} !/Shibboleth.sso/.*$ [NC]

To the .htaccess file, right after turinging on the engine. I have added its own location block in the config file, but as long as allow oeverride is enabled shibboleth gives a 404.

Any help will be apprechated .

Drupal version: 

Source: https://www.drupal.org/taxonomy/term/22/feed