Preheat oven to 350 degrees. Line 18 muffin tin cups with paper liners and set aside.: You should notice the oven steadily warming and a slight hum as it reaches 350 degrees , which creates the even environment needed for consistent rise and texture. Always line the cups to prevent sticking and to make removal effortless, and arrange the tin in the center of the oven so heat circulates uniformly. A common mistake is not preheating long enough, which can lead to uneven baking and dense centers. If your oven runs hot or cold, use an oven thermometer to confirm the temperature, because accurate heat is why your cupcakes will bake through without overbrowning.
In a small bowl, melt butter and chocolate chips together until smooth. Set aside to cool.: As the butter and semi sweet chocolate chips melt, they will combine into a glossy, silky mixture; watch for steam and large unmelted chips which indicate it needs another brief stir. Cooling slightly prevents the eggs from cooking when combined, and it helps the batter emulsify more smoothly. One pitfall is overheating the chocolate making it grainy or burnt; use short bursts in the microwave or a gentle double boiler. The aroma of warm chocolate will deepen as it cools, signaling readiness for the next step.
In a large bowl, whip eggs, sugar and vanilla extract together until ribbons form and color has changed to a light yellow. Stir in melted chocolate and butter. Sift salt, baking soda, baking powder, cocoa and flour together. Slowly alternate the flour mixture and buttermilk into the butter and chocolate mixture, finishing with buttermilk. Scrape the sides to ensure everything is evenly incorporated. Drop by the heaping tablespoon into the lined cupcake pans. Bake 20-25 minutes or until just cooked through. Set aside to cool completely.: The whipped eggs and granulated sugar should look glossy and slightly thickened when you lift the whisk, forming ribbons that fade slowly into the bowl. When you fold in the cooled chocolate, the batter will darken and smell richly of cocoa, creating a cohesive, thick base. Sifting the dry ingredients ensures no lumps of unsweetened cocoa powder or leaveners remain, and alternating with buttermilk keeps the batter smooth and prevents overmixing which would develop gluten and make the cupcakes tough. Drop batter by heaping tablespoons so each cupcake fills evenly; you should hear a faint silence as the batter settles, and the top should spring back slightly when done. Avoid opening the oven during the first part of baking, or they may collapse. Overbaking will dry them out, so check the center for slight bounce rather than a toothpick that comes out completely clean.
For the peanut butter cookie dough, whip butter and peanut butter together until evenly incorporated. Stir in remaining ingredients until combined.: The creamed butter and smooth peanut butter should be pale and fluffy, with a faint nutty perfume. Adding the powdered sugar , brown sugar , all purpose flour , and the splash of vanilla extract transforms this into a cohesive, scoopable dough. The texture should be dense but pliable, not greasy or crumbly; if it feels too loose, a touch more powdered sugar will help. One common error is overbeating which can make the dough too aerated and unstable when pressed into the cupcake cavity. The dough should hold its shape with gentle pressure, making it easy to form into small discs for filling.
Once cupcakes have cooled completely, scoop out a small hole into the center of the cupcakes {about 3/4 inch in diameter and 1/2 inch deep}. Press cookie dough into hole of cupcakes.: Cooling is essential here so the crumb sets and you do not create a funnel to the bottom of the cupcake. When scooping, aim for a shallow, neat cavity that will cradle the peanut butter cookie dough without breaking the walls of the cupcake. The aroma will be faintly chocolatey and the crumb should be tender; press the dough gently so it nests snugly. Avoid scooping too aggressively which can fracture the sides and lead to leaks. If the cavity is slightly larger than intended, press a bit more dough in to form a flush surface for the marshmallow topping.
For the marshmallow tops, place large marshmallows into a large bowl. Microwave until marshmallows start to melt. Stir together and using well greased fingers, remove about 2 marshmallows worth of fluff and place onto cupcake. Squish marshmallow gently down to cover the top of the cupcake. Re-grease hands and continue to cover the remaining tops of cupcakes.: The marshmallows will soften and swell, releasing a sweet, toasted scent as they warm. Work quickly because the mixture will cool and become less pliable; greasing your hands with butter or non-stick cooking spray for your hands prevents sticking and keeps the surface smooth. The marshmallow should form a soft dome that clings to the cupcake edge, and you will feel a slight tack when pressing it down gently to seal. A common mistake is overheating the marshmallows to the point they become too liquid, which makes them hard to shape; warm only until they are soft and pliable for handling.
Once all cupcakes are covered, use a kitchen torch or broiler to toast the tops. Cool slightly and serve.: Toasting will caramelize the marshmallow surface, producing a crackly, maple colored skin and a toasty aroma reminiscent of a campfire. If using a torch, move in steady, even strokes to avoid burning any one spot; under the broiler, watch constantly because the transformation happens in seconds and can quickly go from golden to charred. After toasting, allow them to cool briefly so the marshmallow surface firms and does not stick to teeth. A common pitfall is overtoasting which masks the peanut butter center; aim for golden speckles and a slightly crackled surface to preserve contrast in flavors and textures.