Preheat oven to 325 degrees F (165 degrees C). Grease and dust with cocoa powder three 8-inch round cake pans. Separate the eggs.
Cream 1 cup of the butter and sugar together. Add egg yolks, one at a time, beating after each addition. Stir in 1 teaspoon of the vanilla.
Sift soda, gluten free flour, xanthan gum and 1/4 cup cocoa together. Add alternately with buttermilk to the creamed mixture, beginning and ending with dry ingredients. Stir in the coconut and 1 cup of the chopped pecans.
Beat the egg whites until stiff peaks form and fold into the batter. Pour batter into the prepared cake pans.
Bake at 325 degrees F (165 degrees C) for 25 to 30 minutes. Let cakes cool completely before frosting between layers and on sides.
Frosting: Cream the cream cheese and butter together. Sift confectioner's sugar and 1/4 cup cocoa, beating in a little at a time until well blended. Add 1 teaspoon vanilla and 1 cup pecans.