Preheat your oven to 350°F (175°C). This ensures that your cupcakes will bake evenly and rise beautifully.
In a mixing bowl, whisk together the cupcake flour, cocoa powder, kosher salt, baking soda, and white vinegar. In a separate bowl, beat together the vegetable oil, granulated sugar, egg, vanilla extract, red food coloring, and buttermilk until well combined.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Be careful not to overmix, as this can affect the texture of your cupcakes.
Pour the batter into a lined cupcake pan, filling each liner about two-thirds full. Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean. Allow the cupcakes to cool completely.
In a large bowl, beat the cream cheese and butter together until smooth. Gradually add the confectioners sugar and clear vanilla extract, mixing until the frosting is light and fluffy.
Once the cupcakes have cooled, crumble them into chunks. Layer the crumbled cupcakes and frosting in your jars, starting with a layer of cake, followed by a layer of frosting. Repeat until the jar is filled, finishing with a frosting layer on top.
Refrigerate the jars for at least 30 minutes to allow the layers to set. When you're ready to enjoy, simply grab a spoon and dig in!