So while in game I can press Shift+Enter and I see the ENB menu pop up. But I can't navigate with my mouse or keyboard to the menu. All of my controls still control the game itself but I just happen to see the menu. How do I change the settings in game?

There's another mouse cursor used by the GUI, not your game cursor. It looks like two spinning triangles pointed at each other, or a spinning hour glass.

_________________
AMD Ryzen 5 1600 6C/12T @3.9GHz // 16GB EVGA SSC DDR4 2400MHz // Gigabyte G1 Gaming NVidia Geforce GTX 1060 6GB @ 2050MHz/4104MHz. // Samsung 850 Evo 256GB SSD // 2.5 TB's in HDDs // Windows 10 x64
Lumen ENB
My Flickr