For the Cupcakes: Preheat the oven to 350 degrees F.
Line a standard cupcake tin with paper liners.
In a medium bowl, place the flour, baking powder, baking soda, and salt. Mix until combined.
In the bowl of a mixer fitted with a paddle attachment, add the melted butter.
With the mixer on low, gradually add the sugar. Mix until thoroughly combined (about 2 to 3 minutes).
Add the eggs one at a time. Mixing until just combined.
Add the vanilla and mix.
In a measuring cup, place the milk and lemon juice (or vinegar).
Add the flour mixture and milk mixture in 3 separate steps, starting and ending with the flour mixture.
Fill each cupcake liner only about 1/2 full. We want the cupcakes to be flat when they are baked.
Bake for about 14 minutes or until a toothpick inserted in the center comes out with a few crumbs attached to it.
Remove the cupcake pan from the oven, and allow the cupcakes to cool for about 10 minutes in the pan. Remove the cupcakes and allow them to cool completely on a drying rack.
While the cupcakes cool, make the frosting.
For each frosting flavor, use the following method: In the bowl of mixer fitted with a paddle attachment, cream the butter and sugar until light and fluffy. Add the salt, flavorings, and cream/milk.
Place the chocolate and strawberry frosting flavors in separate bowls. Smooth the top and cover with plastic wrap. Chill until firm.
For the vanilla, keep about 1/2 of the frosting at room temperature, and chill the rest.
While the frosting chills, make the ganache.
Warm the cream until just about to boil.
Pour the cream over the chopped chocolate. Let it stand for a minute or two.
Mix the chocolate and cream until smooth and shiny.
To assemble the cupcakes, put a thing layer of vanilla frosting over the top of each cupcake.
Using a small ice cream scooper, place a single scoop of each flavor frosting on the top of each cupcake.
Drizzle the scoops with ganache.
Place a cherry on top.