The custom menu is NOT the problem. The reason I had to un-publish pages is because deleting them from the custom menu didn’t work. Deleting the entire menu on the Menu page didn’t work. That would be why I’m here. (Just as an FYI, very familiar with WP.)
The site was built by someone other than me using the free template. We bought the pro template. Renamed the free template folder, installed the new template folder. Menu threw up a mess of pages, we lost our Services Page all together and now have a mystery menu that has been deleted in the dashboard and is still showing up on the site. Sorry if I sound a little cranky.