Thanks Jason,
So to clean this up it sounds like I will need to setup a new database and completely strip all the Power CMS code from the sites and start things over. Add CMS to the root site then just add the content access code to each page of the subdomain once the Power CMS system is working.
If there is anything that can shortcut having to completely strip all that code out I would be thrilled to know about it but I'm not holding my breath.