Codeigniter - Setting up SSL and getting 404 errors

I've setup a test SSL certificate using this tutorial. My application requires user authentication. As expected, I get an error message when loading the login page. When I try to navigate to any other page or submit the login form, I get a 404 error message.

My assumption is that all of the URLs since they are created by the controllers, are not being rewritten anymore in the .htaccess. I am unclear how to fix this issue so that all of my URLs work other than the base index.php file.

My server details are as follows:

• Apache2
• Ubuntu 12.04
• Codeigniter 2 (some version of 2)

Here is my .htaccess file:

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /

    #Removes access to the system folder by users.
    #Additionally this will allow you to create a System.php controller,
    #previously this would not have been possible.
    #'system' can be replaced if you have renamed your system folder.
    RewriteCond %{REQUEST_URI} ^system.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]
     RewriteCond %{REQUEST_URI} ^system.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]
    #When your application folder isn't in the system folder
    #This snippet prevents user access to the application folder
    #Submitted by: Fabdrol
    #Rename 'application' to your applications folder name.
    RewriteCond %{REQUEST_URI} ^application.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]

    #Checks to see if the user is attempting to access a valid file,
    #such as an image or css document, if this isn't true it sends the
    #request to index.php
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>

<IfModule !mod_rewrite.c>
    # If we don't have mod_rewrite installed, all 404's
    # can be sent to index.php, and everything works as normal.
    # Submitted by: ElliotHaughin

    ErrorDocument 404 /index.php
</IfModule>