by James McLean.
For anyone looking to do similar I may have a suitable solution (not properly looked into it yet!).
JOOMDLE http://www.joomdle.com
Joomla Extension to integrate moodle with joomla. Awesome potential! Single Sign On, Centralised User Profiles, Hikashop/Virtuemart Integration, etc
For my particular issue, the client should be able to simply create a new Joomla article with specific customer text/logo and then add joomla login module to the page. Joomla ACL structure can then be used to create customer groups thus allowing restriction of available content.
Will mean greater requirements when upgrading, but should hopefully mean no fudging of Moodle core files.