Preheat oven to 350°.
Grease and flour two 9 inch round cake pans and one 6 inch round cake pan.
Stir flours, cocoa powder, sugar, baking soda and salt together in medium mixing bowl.
Whisk flax eggs, coffee, milk, coconut oil and vanilla together in a separate bowl.
Pour liquid ingredients into dry and blend with an electric mixer at high speed for 2 minutes, scraping down the sides of bowl as needed. Batter will be very thin.
Pour batter into cake pans so that your 9 inch layers are of equal thickness and your 6 inch layer is about twice as thick as the 9 inch layers.
Bake each layer until toothpick inserted into the center comes out clean. This will take 20-25 minutes for the 9 inch layers, and 35-40 minutes for the 6 inch layer.
Transfer to cooling rack and allow to cool completely before removing from pans.