Modifying this file I got it to work correctly
/includes/templates/template_default/templates/tpl_checkout_success_default.php

I still can not get it to pull the correct file from either
/includes/templates/custom/checkout_success/tpl_footer.php
/includes/templates/custom/common/checkout_success/tpl_footer.php
Not sure what one is correct but one of those locations should be?

Since my acutal custom templates are located here
/includes/templates/custom/common/tpl_main_page.php and so on.