Preheat oven to 350 degrees. Brush standard muffin tins with butter; dust with cocoa powder, tapping out excess. Whisk together flour, cocoa, baking soda, and salt.
With an electric mixer on medium-high speed, cream butter and granulated sugar until pale and fluffy. Add brown sugar, and beat until fluffy. Add eggs, one at a time, beating until well incorporated and scraping down sides of bowl as needed. Mix in sour cream. Reduce speed to low. Add flour mixture in three batches, alternating with two additions of buttermilk, and mixing until just combined after each.
Divide batter evenly among prepared cups, filling each three-quarters full. Bake, rotating tins halfway through, until tops are firm to the touch and a cake tester inserted in centers comes out clean, about 20 minutes. Transfer tins to wire racks to cool completely before removing cupcakes. Cupcakes can be stored overnight at room temperature, or frozen up to 2 months, in airtight containers.
To finish, drain cherries, reserving 1/4 cup plus 2 tablespoons syrup. Cut each cherry in half. Combine reserved syrup and kirsch in a small bowl. Using a serrated knife (and a gentle sawing motion), split cupcakes in half horizontally. Brush both cut sides with kirsch mixture. Arrange halved cherries over cupcake bottoms; spoon about 1 heaping tablespoon pastry cream evenly over cherries. Replace top halves. Spoon 2 tablespoons glaze over tops. Refrigerate 30 minutes before serving.