Adjust oven rack to middle position and heat oven to 400 degrees. Spray standard-sized muffin pan with nonstick cooking spray. Combine raisins and water in small microwave-safe bowl, cover with plastic wrap, cut several steam vents in plastic with paring knife, and microwave on high power for 30 seconds. Let stand, covered, until raisins are softened and plump, about 5 minutes. Transfer raisins to paper towel-lined plate to cool. If you do not like raisins, feel free to skip this step and leave them out. They are just as wonderful without the raisins.
Process half of bran cereal in food processor until finely ground, about 1 minute. Whisk flours, baking soda, and salt in large bowl to combine; set aside. Whisk egg and yolk together in medium bowl until well-combined and light-colored, about 20 seconds. Add sugar, molasses, and vanilla; whisk until mixture is thick, about 30 seconds. Add melted butter and whisk to combine; add yogurt and whisk to combine. Stir in processed cereal and unprocessed cereal; let mixture sit until cereal is evenly moistened (there will still be some small lumps), about 5 minutes.
Add wet ingredients to dry ingredients and gently mix with rubber spatula until batter is combined and evenly moistened. Do not over mix. Gently fold raisins into batter. Using 1/3-cup measure or ice cream scoop, divide batter evenly among muffin cups, dropping batter to form mounds. Do not level or flatten surfaces of mounds.
Bake until muffins are dark golden and toothpick inserted into center of muffin comes out with a few crumbs attached, 14-18 minutes, rotating pan halfway through baking. Cool muffins in pan for 5 minutes, then transfer to wire rack and cool for 10 minutes before serving.
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