Heat oven to 350 degrees. Line 12 standard muffin tins with paper cupcake liners.
Pick out 12 of the prettiest freeze dried raspberries and set aside to garnish the cupcakes, keep them sealed in a plastic bag until ready to use. Place the rest in a plastic bag and roll with a rolling pin until crushed into coarse crumbs.
In a large mixing bowl whisk together the brown rice flour, coconut flour, tapioca starch, cocoa powder, baking powder, baking soda, salt and crushed raspberries.
In another mixing bowl whisk together the yogurt, apple sauce, milk, eggs, 1 teaspoon vanilla, oil and coconut sugar. Add the wet ingredients to the dry ingredients and combine well. Divide the batter evenly among the prepared muffin tins. Bake for 25 minutes or until they feel firm to the touch and a tooth pick inserted in the center comes out mostly clean. Let cool in the pan for 5 minutes then remove to a wire rack to finish cooling.
Bring the agave to a boil in a heavy saucepan and continue to boil for 3 or 4 minutes or until big fat bubbles form (225 degrees on a candy thermometer).
While the agave is cooking, beat the eggs whites with 1/8 teaspoon of salt until stiff peaks form. Carefully pour the agave into the egg whites with the mixer on low speed. After all the agave has been added, increase the speed to medium-high and continue beating until the frosting is completely cool, about 7 minutes. The frosting should be thick, glossy and smooth. Sift the cocoa powder into the frosting and beat on medium-high just until the cocoa has been incorporated. Use a spatula to ensure all the cocoa has been thoroughly combined.
To assemble, frost the cooled cupcakes with the frosting and garnish with the reserved raspberries.