Adjust an oven rack to the lower third position and preheat the oven to 350 degrees.
Line a 12-cup standard-size muffin pan with cupcake liners.
Assemble all ingredients.
In a medium-size bowl, whisk together the flour, cocoa, baking soda, and salt.
Combine the buttermilk, food color, and vinegar in the measuring cup.
Beat the butter and shortening in a stand mixer with the flat beater on medium speed until creamy, about 1 minute.
Add the brown sugar and vanilla and beat in well.
Gradually add the granulated sugar—sprinkle it in slowly and steadily—while beating on medium speed.
When all the sugar has been added, scrape the bowl and beater and beat 4 minutes on medium-high speed. The sugar and butter will climb up the sides of the bowl, so stop 2 or 3 times to scrape the bowl down. The mixture will look fluffy.
Beat in the eggs on medium speed one at a time just until smooth.
On low speed alternately add the dry ingredients in 3 additions and the liquid in 2 additions, beating only until smooth. At first the batter may look curdled.
But after all the ingredients are incorporated it will look smooth and creamy.
Divide the batter into the prepared pan using two soup spoons or an ice cream scoop.
Bake about 25 minutes, until a toothpick inserted into the center of a cupcake comes out clean. Tops of cupcakes will spring back when gently pressed.
Cool cupcakes in the pan 10 minutes, then remove them and cool completely on a wire rack.
For the frosting, beat the cream cheese, butter, and vanilla on medium speed with the flat beater only until smooth and creamy. Scrape bowl and beater often.
Add the strained confectioners’ sugar and beat on low speed until completely incorporated and frosting is smooth and thick. Don't beat on high speed or the frosting will be too airy.
Either frost the cupcakes with a narrow-bladed metal spatula or pipe the frosting through a pastry bag with a star tip.
Let stand until set, about 1 hour. Cupcakes are best when very fresh.
Store leftovers in a tightly covered container. I wash and dry the clear deep rectangular plastic boxes (1-pound size) that held organic spinach or salad mix and use them.