Preheat the oven to 350 degrees F (175 degrees C). Grease two 9-inch round cake pans and line with parchment paper.

Spread coconut flakes thinly over a microwave-safe plate. Microwave on high until lightly browned, stirring every 30 seconds, 2 to 3 minutes total.

Place coconut in a blender and grind into a fine powder.

Combine coconut powder, buttermilk, and vanilla extract in a bowl. Combine cake flour, baking powder, salt, and baking soda in a separate bowl.

Beat sugar, butter, and shortening until fluffy. Add eggs, one at a time. Add flour mixture alternately with coconut-buttermilk mixture, mixing between additions. Mix in pecans. Divide batter between the pans.

Bake in the preheated oven until a toothpick inserted into the centers comes out clean, 28 to 32 minutes. Cool cakes in pans for 10 minutes. Remove cakes from pans and cool on wire racks, at least 20 minutes.

Meanwhile, beat powdered sugar and butter until fluffy. Mix in cream of coconut, vanilla extract, and salt. Add cream cheese; beat until well combined. Place 1 cooled cake on a serving platter and spread frosting all over. Place the other cake on top; coat with remaining frosting.

Press remaining pecans around and on top of the cake to garnish.