In a large mixing bowl, beat the eggs on a high speed until they are pale and frothy. Add the sugars and beat on high until thick and pale. Gradually add in the butter and vanilla extract until it is combined well.
Combine the cocoa powder, flour and salt on a low speed until it is incorporated, then turn the speed up to mix it very well.
Use a mixing spoon to stir in the chocolate chips.
Divide the batter evenly into the cupcake molds on top of the graham crust. Bake for 30 minutes, until the brownies have risen, but are still fudge-y in the center. Remove and let cool to room temp before spooning or piping on the marshmallow fluff.
Use a kitchen torch or broiler set on high to toast the marshmallow in the oven. If toasting in the oven, this should take no more than 60 seconds, depending on how high the rack is set in your oven.
Serve right away or store at room temp until ready to eat. The marshmallow fluff will likely spread and drip over the edges of the cupcake as it sits. If this doesn't appeal to you, use mini marshmallows instead.