I logged in and tried to do a backup using the Duplicator plugin but it doesn’t support it. I see you are using a WordPress.com installation of WordPress.
I think it may be better for you to create a seperate install of WordPress, install the new version theme and then migrate your changes over. Or if you have full access to your hosting panel I can do it that way. I need access to the database and the files in order to make a backup.
As for the menu, view our demo and you will see what I mean, http://demo.themely.com/integral/
If you want to add more padding on the logo you can do it in the style.css file.