Make the filling: combine evaporated milk, egg yolks, brown sugar, and butter in a saucepan over medium heat. Cook, stirring constantly, about 12 minutes until thickened to pudding consistency. Stir in toasted coconut, pecans, and vanilla. Cool completely.
Preheat oven to 350°F (177°C). Grease and line three 8-inch cake pans.
Whisk together flour blend, extra xanthan gum, cocoa powder, baking soda, and salt.
Beat butter and sugar for 3 minutes until pale and fluffy. Add eggs one at a time, beating well after each. Mix in melted chocolate and vanilla.
Add the dry mixture in three additions, alternating with buttermilk, starting and ending with dry. Mix on low just until combined.
Divide batter evenly between pans. Bake 22–25 minutes, until a toothpick comes out with a few moist crumbs.
Cool in pans 10 minutes, then turn out onto a wire rack and cool completely, at least 1 hour.
Spread cooled coconut-pecan filling between each layer and on top. Slice and serve.