Preheat the oven to 300 degrees. Lightly spray the cups of a 12-cup muffin pan with nonstick spray oil or line them with paper or foil muffin cups.
In a medium bowl, combine the hot water and molasses, stirring until well blended. Add the milk and mix to combine.
In a large bowl, sift together the flours, sugar, baking powder, baking soda and salt.
Use a spatula to fold the liquid mixture and pecans into the dry ingredients just until the flour is incorporated; do not overmix. (The batter will be dark mocha-colored and dense.) Fill the cups almost to the top and bake for 45 minutes to 1 hour, until the muffins are set. Serve warm.