This WP install is not at the root because it was still under development. I tried to install the Jim Morgan wordpress and upon hitting submit, I stopped having access to the page, and all wp-admin, and the entire domain, including the parent directory which is not even using WP.
I went into the site via FTP and did not find any new .htacess files. There was one there, but it was last modified in April and had no code inside of it.
I have a lot of experience using .htaccess. Usually you can simply delete the file and start over. But if there is no file, how do your restore it?