After looking into this more (more awake) I have found two things.
1. somehow a duplicate of the common folder wound up outside the admin folder. I renamed this folder to take it out of the structure.
2. most or all paths are wrong in regard to images and function such as the add content button.
I proved this out by looking at the image properties in the CMS while on the server and changed the path to what it should be according to the directory structure and the image did appear.
How can I make sure that all paths are correct for all pages in the CMS?
Does this require an install of all files again, if so how does that affect the database?
Thanks for your help