Preheat oven to 425°F. Line or grease a 6-cup muffin pan and set aside.
Combine vinegar and milk and set aside to curdle.
In a large bowl, sift or whisk together pastry flour, almond flour, cocoa powder, sugar, instant coffee, baking soda, baking powder, and salt.
In a separate bowl, combine applesauce, peanut butter, vanilla, and milk/vinegar mixture.
Make a small well in the middle of your flour bowl and add in wet ingredients. Gently fold together wet and dry ingredients until almost combined, add in the chocolate chunks if using, and fold a couple more times until just combined.
Divide batter evenly among muffin cups and place in oven. Bake for 5 minutes, then lower the temperature to 350°F and continue baking for another 15-20 minutes, or until a toothpick inserted in the center comes out clean.
Let the muffins cool in the pan for 5 minutes, then transfer to a cooling rack to cool completely.
*These muffins are very lightly sweetened. For a more traditional sweet muffin, add up to 1/2 cup.