First, preheat oven to 350° Fahrenheit. Line two cupcake pans with paper cupcake liners and set aside. In a food processor, or nutribullet, blitz up the gluten free graham crackers to a fine crumb. Dump crumbled crackers into a medium bowl and mix in the melted butter, salt, and sugar until the mixture looks like wet sand. Scoop a near-tablespoon of the mixture into each of the lined cupcake cups and press down with your fingers until a crust is made. Bake for 5-7 minutes and then remove and let cool.
While the crust is baking, make the cupcakes. In a large bowl, whisk together the flour, sugar, baking soda and powder, salt, and cocoa powder. Then, in another large bowl, whisk together the eggs, sour cream, vanilla, oil, and melted semi-sweet chocolate until smooth. Pour in the whisked dry ingredients and stir entire mixture until combined. Add in the hot coffee and mix. Then stir in the chocolate chips. Spoon out the mixture into the cupcake cups on top of the graham cracker crust - each cup should be 3/4 to nearly full. Bake for 20-26 minutes. Less time will yield fudgier brownie cupcakes, longer will give you cakeier cupcakes (I usually go for fudgier at 20-22 mins). Remove and let cool.
While the cupcakes are baking, make the marshmallow fluff. In a small saucepan, combine the water, corn syrup and sugar over medium heat. Stir occasionally until all of the sugar dissolves, and then stop stirring immediately and let simmer (turn down to med-low heat). Insert your candy thermometer to check temp - this will take 5-10 minutes. Let the mixture simmer (do NOT stir it) until it reaches 240 degrees Fahrenheit (softball stage). While the mixture is cooking, make the meringue.
In a large, perfectly clean, dry bowl, begin beating your room temp egg whites with your electric mixer. If there is any oil or crumbs in the bowl, the egg whites will not get stiff, so make sure all implements are clean and dry. Beat egg whites until foamy and then add in the cream of tartar and continue to beat until soft peaks form. Let sit until your sugar mixture has reached softball stage.
Once the sugar syrup is at 240 degrees, immediately turn off heat, and, using heat pads (or a friend to help!), start beating egg whites again and slowly pour in the hot sugar mixture into the egg whites. Beat constantly until all of the sugar mixture has been added (pour in a slow stream, do not dump it in). Do not stop beating the egg whites! Continue to beat after all the sugar syrup has been added, until the bowl is back to room temperature (it will be very hot after adding the syrup). You can add a bag of frozen peas under the bowl or on the side to help cool the bowl as you beat the mixture. This will take 10 or so minutes, so be patient. As the bowl cools, the mixture will become thicker and stiffer and stickier as the marshmallow forms!
Once the bowl is room temp, you can stop beating the marshmallow. Scoop it into a piping bag and pipe onto the cooled cupcakes (the fudgier cupcakes will fall in the center which makes a great pocket for more marshmallow fluff!). Optional step: toast the marshmallow topping once piped with a culinary blow torch!