Preheat oven to 350 degrees. Line two 12-cup muffin pans with 18 paper liners. Soak raisins in 1 cup hot water until soft, about 10 minutes; drain raisins and transfer to a food processor. Puree until smooth, about 30 seconds.
In a medium bowl, combine bran, flours, baking powder, baking soda, and salt. In a large bowl, stir together yogurt, brown sugar, molasses, butter, egg, and raisin puree. Add dry ingredients and stir to combine; fold in pineapple. Divide batter evenly among liners. Bake until a toothpick inserted in center of a muffin comes out clean, about 25 minutes, rotating pans halfway through.