So, you've followed this guide to a T and now you're ready to export. Here are some notes before you export:
Selected Objects - This allows you to export only the objects you have selected. Highly recommended to toggle it on so you don't accidentally export the whole scene.
Apply Scalings - Set this to FBX All This fixes some scaling issues in Unity.
!EXPERIMENTAL! Apply Transform - This also fixes scaling issues in Unity, but primarily in regards to armatures. Just toggle it on anyway.
No Leaf Bones - Turn off "Add Leaf Bones". It adds useless additional bones to the ends of armatures.