Preheat the oven to 392°F (200°C) and line the pan with liners. Set aside.
Stir the milk and vinegar together. Set aside.
In a bowl, whisk together the flour, baking powder, nutmeg, baking soda and salt. Set aside.
In another bowl, whisk together the oil, vanilla, sugar and kahlua.
Add the the oil mixture to the flour mixture and whisk together.
Fold in the chocolate chips.
Fill each muffin liner with the batter, about ¾ full (I use a cookie scoop).
Sprinkle the tops with more chocolate chips, if desired.
Bake for 5 minutes and then lower the temperature to 356°F (180°C) and bake for another 15-20 minutes or until a toothpick inserted in the middle of a muffin comes out mostly clean.
Let the muffins cool in the pan for about 5 minutes before transferring them to a wire rack to cool completely.
Store the muffins in an airtight container at room temperature for about 4 days or in the refrigerator for about a week.