It looks like the root URL settings need to be updated. In you CSSMenuWriter folder open up the menu.php file. At the top you should see the URL values. It looks like it is adding a web/gbftacoma.org/ to the links, so if you see this in the URL values you should remove it.
If you have the files with the menu in the root of the site these URL's should be set to /. If you have any trouble with this post back with this menu.php file.