Heat oven to 350°. In a large double boiler over simmering water, melt sugar, chocolate, butter, and water, and whisk well to combine. Let cool to room temperature. Stir in milk, vinegar, eggs, and vanilla, and set aside. In a separate bowl, whisk together flour, baking soda, baking powder, and salt. Fold into chocolate mixture.
Pour to the rim of lined muffin tins and bake 15 to 20 minutes (tops will spring back when lightly touched). Let cool completely, and top with Vanilla Frosting.
Adapted from Joanne Chang, Flour Bakery & Cafe
In a medium bowl, combine ingredients until smooth.