Programmatically render menu on search view
I worked it out, turns out the problem is different to what I thought.

Because the search view isn't in the menu structure I need to add different values to the $config array. Firstly I needed to add "parent_mid" so it knew what menu item to use as the root for the menu tree &amp; I needed to change the level to 1 to output the links I wanted. Although 2 was still outputting links, just the wrong ones for what I needed.

If you need to work out what the parent_mid is go to Admin > Structure > Menus > Your Menu &amp; hover over the edit link for the menu item you want to be the root of the menu tree, the ID is in the URL. You can also get it programatically, like I did, using menu_node_get_links().