For the cupcakes: Preheat the oven to 350˚F. Line muffin pans with paper liners.
Boil 5 cups of water and pour into a medium bowl.
Place the chocolate chips and butter into a smaller bowl, and place it into the bowl full of water. Mix the chocolate chips and the butter until the mixture is smooth, making sure not to let the water mix in with the chocolate mixture.
Whisk in the brown sugar until fully combined. Mix in the eggs, 2 teaspoons of vanilla, flours and chocolate chips until fully incorporated.
Scoop the batter into the prepared pans, and bake for 25 minutes, or until a toothpick inserted comes out with only a couple of crumbs.
Let cool in the pan for around 5 minutes, then remove to cool completely on wire racks.
For the frosting: Beat together the peanut butter and the butter until light and fluffy. Mix in 1/2 teaspoon of vanilla.
Add the powdered sugar 1 cup at a time, alternating with 1 teaspoon of milk until it reaches your desired consistency. Beat until light and fluffy. Pipe onto cupcakes.