Preheat oven to 325 degrees. Thoroughly grease a 12-cup muffin pan. In a medium bowl, stir together flour, baking soda and baking powder.
In a large bowl, beat the butter with an electric mixer on high speed until creamy. Gradually add the sugar and beat for 5 minutes or until fluffy. Add one egg to the mixture and beat until combined. Repeat for the remaining two eggs. With the mixer on low speed, add the following ingredients, one at a time, while ensuring that each is incorporated before adding the next: half of the flour mixture, yogurt, remaining flour mixture, orange juice and orange zest. Scrap the bowl as needed when mixing in the ingredients.
In a medium bowl, create the crumb mixture by combining graham crackers, brown sugar, cinnamon, nuts and butter.
Put two tablespoons of batter into the bottom of each muffin cup. Evenly spread one tablespoon of the crumb mixture on top of the batter. Divide the remaining batter among the 12 cupcakes, ensuring that the crumb mixture is completely covered. Spread the remaining crumb mixture evenly on the top of each cake.
Bake at 325 degrees for 35 to 40 minutes, or until golden brown and a toothpick inserted in the center of each cake comes out clean. When done, remove from oven and allow to cool on a wire rack. Carefully remove each cake from the muffin pan.
In a small bowl, stir together the powdered sugar, orange juice and orange zest. If necessary, add additional orange juice to reach desired consistency. Spoon equal amounts on top of each cake.