1. Preheat oven to 375°.
2. Weigh or lightly spoon flours into dry measuring cups; level with a knife. Combine flours, cocoa, and next 4 ingredients in a bowl; stir with a whisk.
3. Place sugar and 1/4 cup butter in a large bowl; beat with a mixer at medium speed until blended. Add eggs, 1 at a time, beating well after each addition. Beat in sour cream and vanilla. Gradually add flour mixture, beating at low speed until smooth (batter will be very thick).
4. Place 12 paper muffin cup liners in muffin cups; coat liners with cooking spray. Spoon batter into prepared cups (cups will be almost full). Bake at 375° for 20 minutes or until a wooden pick inserted in center comes out clean. Cool 10 minutes on a wire rack; remove from pan. Cool completely on wire rack.
5. Combine powdered sugar, 2 tablespoons butter, milk, and 1/2 teaspoon vanilla in a medium bowl; beat with a mixer at low speed until blended. Increase speed to medium; beat until smooth. Spread frosting over cupcakes.