Make the Graham Cookies: Position a rack in the center of the oven and preheat the oven to 375 degrees F. Line two baking sheets with parchment paper.: Position a rack in the center of the oven and preheat the oven to 375 degrees F. Line two baking sheets with parchment paper. : You will notice a warm bakery smell as the oven heats and the parchment laid out makes cleanup simple. Preheating ensures even oven spring, and positioning the rack centrally gives the cakes room to dome without browning too fast on the bottom. A common mistake is putting the rack too low, which can cause overly browned undersides, so double check placement first.
In a medium bowl, stir together both flours, baking powder, and salt.: As you whisk, the mixture will develop a uniform sandy texture and you may see small clumps that disappear with whisking. This dry mix ensures even distribution of leavening so each cake rises the same way. Avoid mixing wet and dry too vigorously later, since overmixing the batter can lead to tough cakes.
In the work bowl of a stand mixer fitted with the paddle attachment, beat together the butter, shortening and brown sugar until light and creamy, about 3 minutes. Add the eggs and the buttermilk and beat until combined.: The butter and sugars aerate into a pale, creamy mass, and you will hear the mixer change tone as it becomes fluffier. Adding eggs and buttermilk next creates an emulsion that yields a tender crumb. If you skip proper creaming, the cakes may be dense, so scrape down the bowl to ensure everything is fully combined.
In a measuring cup, combine the milk, baking soda, and vinegar. Add the milk mixture to the batter along with the flour mixture and beat on low speed until just combined. Add the vanilla and beat on medium speed for about 2 minutes, until completely combined.: When the milk mixture hits the batter you may see small bubbling as the baking soda activates, which helps create lift. Folding the dry ingredients in gently prevents gluten overdevelopment, while the final beat smooths the batter to a uniform sheen. Be careful not to overmix, or the cakes will lose their tenderness and become chewy.
Using a spoon, drop about 1 tablespoon of batter onto one of the prepared baking sheets and repeat, spacing them at least 2 inches apart. Bake one sheet at a time for about 10 minutes each, or until the cakes begin to brown. Remove from the oven and let the cakes cool on the sheet for at least 5 minutes before transferring them to a rack to cool completely.: The batter should fall in a slightly rounded mound that flattens a touch as it spreads. In the oven you will hear gentle bubbling and see the edges firm while the centers remain soft, a sign they are done. Leaving them on the baking sheet allows residual heat to finish cooking. Resist the urge to move them immediately, as they can tear if transferred too soon.
Make the Chocolate Ganache Filling: Put the chocolate in a large, heatproof bowl. Heat the cream in a large, heavy saucepan over medium heat just until it bubbles. Pour the hot cream over the chocolate in the bowl and let it sit for about 10 minutes, until the chocolate is melted. Stir with a wooden spoon or spatula until smooth. Allow the mixture to rest at room temperature until firm enough to spread, about 2 hours. You may also refrigerate the mixture for about 30 minutes, until it is firm enough to spread, stirring every 10 minutes.: Put the chocolate in a large, heatproof bowl. Heat the cream in a large, heavy saucepan over medium heat just until it bubbles. Pour the hot cream over the chocolate in the bowl and let it sit for about 10 minutes, until the chocolate is melted. Stir with a wooden spoon or spatula until smooth. Allow the mixture to rest at room temperature until firm enough to spread, about 2 hours. You may also refrigerate the mixture for about 30 minutes, until it is firm enough to spread, stirring every 10 minutes. : As the hot cream softens the chocolate , you will see glossy ribbons form when you stir, and the aroma will deepen to a rich cocoa scent. Resting the ganache lets it thicken to a spreadable consistency so it does not ooze from the whoopie pies. Avoid overheating the chocolate in the microwave, which can cause grainy texture; gentle, even heat is key.
Make the Marshmallow Filling: In the work bowl of a stand mixer fitted with the paddle attachment, beat together the Marshmallow Fluff and the vegetable shortening, starting on low and increasing to medium speed until the mixture is smooth and fluffy, about 3 minutes. Reduce mixer speed to low, add the confectioners' sugar and the vanilla, and beat until incorporated. Increase mixer speed to medium and beat until fluffy, about 3 minutes more.: In the work bowl of a stand mixer fitted with the paddle attachment, beat together the Marshmallow Fluff and the vegetable shortening, starting on low and increasing to medium speed until the mixture is smooth and fluffy, about 3 minutes. Reduce mixer speed to low, add the confectioners' sugar and the vanilla, and beat until incorporated. Increase mixer speed to medium and beat until fluffy, about 3 minutes more. : The mixture will transform from glossy and sticky to soft peaks that hold shape, and the scent will be sweet and vanilla forward. The shortening stabilizes the filling so it spreads cleanly between cakes and resists weeping. A typical misstep is adding the sugar too quickly, which can create dusting or lumps, so add it gradually.
Assemble the whoopie pies: Pipe or spread (whatever your preferred method) a layer of chocolate ganache filling onto the flat side of one of the cakes. Using the same method, top the chocolate filling with the marshmallow filling. Top it with another cake, flat-side down. Repeat with the rest of the cakes and filling.: Pipe or spread (whatever your preferred method) a layer of chocolate ganache filling onto the flat side of one of the cakes. Using the same method, top the chocolate filling with the marshmallow filling. Top it with another cake, flat-side down. Repeat with the rest of the cakes and filling. : When assembling, press gently so fillings meet the edges without squishing out, and you will hear a faint give as the cakes nestle together. The contrast of glossy ganache and billowy marshmallow is visually appealing and offers a pleasant mouthfeel. A common error is overfilling, which makes the whoopie pies messy, so use a measured dollop for consistent results.
