Move the oven rack to the middle position and preheat the oven to 400 degrees F. Line a standard muffin tin with paper liners or spray the tin with nonstick cooking spray.
Next, place the raisins and water in a small microwave-safe bowl and cover it with plastic wrap. cut 3 steam vents in the plastic. Microwave on high for 30 seconds. Keep the raisins covered until they are plump and softened about 3-5 minutes.
Then, place half of the bran cereal in a food processor and process until ground into a flour, about 10 5-second pulses; set aside.
In a large mixing bowl whisk together the cake flour, whole wheat pastry flours, baking soda, and salt; set aside.
In a medium bowl whisk together the egg and yolk until lightened in color, about 30 seconds. Whisk in the sugar, molasses, and vanilla until the mixture is thick and combined. Then, whisk in the melted and cooled butter until combined followed by the yogurt. Next, whisk in the processed All-Bran cereal and unprocessed bran cereal, and let the mixture sit until the cereal is moistened about 15 minutes.
Whisk the wet ingredients into the dry ingredients until combined being careful to not over-mix. Fold in the raisins and walnuts.
Use a 1/3-cup measuring cup or ice cream scoop to scoop the batter evenly month the muffin cups. Keep the batter domed—do not level it off. Bake until a toothpick inserted into the center of the muffins comes out with just a few moist crumbs, about 16-20 minutes, rotating the pan halfway through baking.
Place the muffin tin on a wire rack for 5 minutes, and then remove the muffins from the tin and place them on the wire rack to cook an additional 15 minutes before serving.