Preheat oven to 375°F. Line muffin pan with paper liners.
Stir hot water and instant coffee together in a large mixing bowl. Add buttermilk, canola oil, fat-free sour cream, egg and egg substitute, and vanilla. Whisk until well blended.
Add flours, sugar-substitute, brown sugar, cocoa, baking powder, baking soda, and salt to another large bowl and whisk to blend well. Stir in the buttermilk mixture, stirring only until just combined. Mix in chocolate chips and pecans.
Spoon the batter into the prepared muffin cups using a 1/4-cup measuring cup. Bake until tester comes out clean (about 25 minutes).