In a mixing bowl, whisk together all purpose flour, graham flour, baking powder, salt and cinnamon, set aside. In a separate mixing bowl, using an electric mixer, whip together butter, brown sugar and honey until pale and fluffy. Stir in eggs and vanilla extract, scraping down the sides of bowl as needed. Add in dry ingredients and mix just until combine.
Divide batter evenly among 12 paper lined muffin cups, each cup should be about 2/3 full. Bake in preheated oven 21 - 24 minutes until toothpick inserted into center comes out with a few moist crumbs attached.
Allow muffins to cool completely before topping with ganache and toasted marshmallows.
For the Chocolate Ganache:
Combine chocolate chips and heavy cream in a microwave safe bowl, microwave on 50% power in 30 second intervals, stirring after each interval until melted and smooth.
For the Toasted Marshmallows:
Place oven rack two levels below oven broiler and preheat oven to low-broil. Generously butter a cookie sheet as well as a silicon or rubber spatula, set spatula aside.
Spread miniature marshmallows in an single layer close together, in the center of the cookie sheet (if using 12 large marshmallows align in a single layer several inches apart from each other so they don't stick together). Place cookie sheet in oven and toast marshmallows until golden, rotating pan as needed to evenly toast marshmallows (this may take only a few seconds, so watch them closely the entire time).
Once golden, immediately remove from oven and use buttered spatula to scoop up small bunches of marshmallows at a time and lift onto ganache covered cupcakes (if using 12 large marshmallows, just scoop and place 1 large marshmallow on each cupcake).
To Assemble the Cupcakes:
Spread about 2 1/2 tsp thick chocolate ganache over each cooled cupcake, followed by toasted marshmallows.**
Store cupcakes in an airtight container.
Notes
*You can use mini marshmallows or regular marshmallows for this recipe (although regular sized marshmallows are easier to toast and slide off the baking sheet).
**Note: I have made these muffins twice and both times about 1 tsp of the center of the cupcake didn't rise level with the rest but it turned out it worked perfectly to have a ganache filled center, if yours do rise level then cut a small hole in the center of each cupcake about the size of a teaspoon to fill with ganache.