I just checked out your paper here: http://news.getcleantech.com/#/ and note that you have turned on your custom header. This means that you have hidden all paper.li menus from your readers (i.e. you have turned on "white labeling"). To view the paper.li menus and sign in as the publisher, navigate to your paper URL, click ESC on your keyboard and you'll be asked to sign in. Once signed in to your domain, you will see the paper settings cog, top right to view your paper settings again as well as the main menu icon, top left.
Hope that helps!