In a medium-size bowl combine the hot water and molasses, stirring until well blended. Stir in the milk until blended. In a large bowl sift together the flours, sugar, baking powder, baking soda and salt.
With a rubber spatula, fold the liquid mixture and the pecans into the dry ingredients just until flour is thoroughly incorporated; do not over mix. Spoon into 12 greased muffin cups. Bake at 300F until done, 45 minutes to about 1 hour. Remove from pan immediately and serve while hot.