Thanks guys. I was able to get the site running by NOT putting an .htaccess file in the root directory. Silly I know.
Peter, I have not has this issue prior to this version of WP either. This was a fresh install of WordPress 3.9.1 so I figured that it was an error in the programming when I found the .htaccess in the uploads sub-directory. I will add that code just in case.
Every time I did put a copy of the .htaccess into the root, it would cause everything I clicked on in the dashboard to attempt to open a php file rather than to execute an action.
I’m not happy with how it is working at the moment BUT it is working.
My concern now is that when WP updates again that things will run amok with the current set-up and create a whole new set up headaches for this client.
