The first thing you must do is changing the height of your #top. Once you see the logo fits in there you can adjust the top of the #mainmenu. The #mainmenu is only hovering over the #top and does not give your logo more space.
I’ve added an option in the latest update of this theme (v5.0) that enables you to adjust the header height in the theme settings. If you haven’t made any other changes to the theme code then you can use the new update instead 🙂