Preheat oven to 350°F. Line a muffin tin with cupcake liners.
Crush graham crackers in food processor. In a small bowl, combine the flours and ground graham crackers. Set aside.
In a large bowl cream the butter and sugar until fluffy. Beat in the eggs and vanilla. Add half of the flour mixture and half of the milk and mix. Add in remaining flour and milk and mix until batter is smooth.
Spoon the batter into the cupcake liners, filling them about 2/3 full. Bake for 20 to 25 minutes, or until tops are golden and a cake tester inserted into the center of the cupcake comes out clean. Cool cupcakes before frosting.
While cupcakes cool, make the chocolate ganache. Place chopped chocolate in a bowl. Boil heavy cream and pour on top of chopped chocolate. Whisk until smooth. Brush a thin layer of chocolate ganache on top of each cupcake. Then place mini marshmallows over top, covering cupcakes. Bake for an additional 5 minutes until marshmallows are toasted.
The nutrition information provided are only estimates based on an online nutritional calculator. This is not a comprehensive list of all the nutrients in the recipe (i.e., does not include vitamins, cholesterol, etc). I am not a certified nutritionist. Please consult a nutritionist or doctor for accurate information and any dietary restrictions and concerns you may have.