How to change the shortcuts of the side menu. For example, to add recent changes, special pages ...etc. Also the preferences page is currently empty.
Topic on Skin talk:Minerva Neue
Looks like you can't (I was missing recent changes as well). Try the Timeless Skin instead that one offers recent changes and special pages.
IF wfLoadSkin( 'Timeless' ); throws an error on your wiki, be sure to include $wgMFDefaultSkinClass = "SkinTimeless"; in your LocalSettings.php as well.