Preheat oven to 350F. Place 15 cupcake liners in 2 muffin pans and set aside.
To make the cake, whisk together the flour, cocoa, sugar, salt, baking powder, and baking soda in a large bowl.
Add in the nondairy milk and oil, and mix vigorously. Add in the vinegar and vanilla, and mix until well combined. Finally, stir in the peanut butter.
Divide the cake batter between the prepared cupcake liners, and bake for 17-20 minutes, until a toothpick inserted in the center comes out with just a few crumbs. Set aside to cool completely before filling.
To make the peanut butter frosting, combine the vegan butter, vegan shortening, and peanut butter in the bowl of a stand mixer fitted with the paddle attachment. Beat until smooth and creamy, then add in the vanilla.
Mix in the powdered sugar, one cup at a time until frosting is thick and holds its shape. If it is too thick, add some nondairy milk to smooth it out.
Repeat the same exact process for the chocolate frosting!
To frost, see one of the methods of 2-color frosting I mentioned above and frost cupcakes as desired. Top each with a ¼ of a peanut butter cup. Enjoy!!