Step 1 Heat the oven to 350 degrees. Line standard-sized muffin trays -- two trays unless you have a very large one -- with paper muffin liners. Sift the graham and all-purpose flours, baking powder, salt, cinnamon and allspice into a large bowl and set aside
Step 2 In the bowl of a standing mixer fitted with a paddle attachment, cream the softened butter, sugar and honey on high speed until creamy and light, about 3 minutes. Turn the speed down and add the vanilla and the eggs, one at a time, occasionally scraping down the sides of the bowl.
Step 3With the mixer turned to low, slowly add the dry ingredients to the butter mixture, mixing only until combined. Add the chocolate and mix just until combined.
Step 4Spoon the batter into the lined muffin pan cups, about one-third cup each. Bake until the tops are dark golden brown and a toothpick comes out clean, 20 to 24 minutes. Cool the cupcakes on a rack while you make the frosting.