Preheat the oven to 375-degrees. Whisk together the flour, cocoa, baking soda, salt and sugar into a large bowl. In separate bowl, measure and mix the oil, coffee, bourbon, and vanilla. Slowly pour the liquid ingredients into the bowl and mix the batter with a whisk.
When the batter is smooth, add the vinegar and stir quickly. There will be pale swirls (and some bubbling) in the batter where the baking soda and vinegar are reacting. Stir just until the vinegar is evenly distributed throughout the batter (the color becomes more consistent throughout).
Pour batter into a lined muffin tin and bake for 25 minutes–testing with a toothpick. Remove and place to cool on a baking rack.
In a small sauce pan, heat up the milk and the chocolate. Stir often until melted. Add more milk if needed. Mix in the corn syrup, bourbon and salt and stir until blended and until the ganache reaches an almost spreadable consistency. Let cool. The ganache will thicken up slightly and spread on your cupcakes. Sprinkle with sprinkles.