Make the cupcakes: In a small saucepan over medium heat, melt the sugar, butter, salt and water, stirring as needed. Place the chocolate and cocoa powder in a medium bowl; pour the butter mixture over and whisk till the mixture is smooth. Whisk milk, egg, yolk, vanilla and chocolate flavor (if using) into chocolate mixture till combined.
In medium bowl, whisk together flours, stevia, baking powder and baking soda; add to chocolate mixture and whisk till smooth. Let batter sit at room temperature for 1 hour, or cover and refrigerate for up to three days.
When ready to bake cupcakes, remove batter from fridge and set oven to 350F. Line a 12-cup muffin tin with paper liners. Use about 3 Tbsp. batter for each cup. Bake about 17-22 minutes, or till a toothpick inserted near center returns with a few crumbs. (My cupcakes took 19 minutes.) Transfer cupcakes to a wire rack to cool completely before filling and frosting.
Make the frosting: In medium bowl, beat butter and peanut butter on low speed to smooth and well combined. Sift sugar and cocoa powder together. Gradually add to butter mixture with the yogurt, mixing on low, then on medium speed after each addition till mixture is again smooth. Add Kahlua (or coffee if using). If frosting is too thin at this point, add up to 1/2 cup additional sifted sugar to bring it to frosting consistency. Add melted chocolate, and beat mixture on medium-high till smooth and well combined. Yield: enough to generously frost 12 cupcakes.
Assemble the cupcakes: Scoop the centers of the cupcakes with a serrated spoon or Cuisipro cupcake corer. Use discarded cupcake pieces for snacks. Transfer peanut butter to a resealable sandwich bag. Snip end of one corner to make a 1/2” – 3/4” hole through which you will pipe the peanut butter into the cupcake cavity. Frost cupcake with swirls using a Wilton 1M or 2D decorating tip, or apply frosting with a knife. Garnish with crushed honey-roasted peanuts, if desired.
TIP: Don’t discard the egg white! Add it to your scrambled eggs, or freeze it to use for marshmallow frosting or Swiss Buttercream frosting.