Preheat the oven to 350°Line a 12-cup cupcake pan with paper liners.
In a medium bowl, whisk together the flour, baking soda, and salt. In a small bowl, stir together the milk, molasses, and vanilla.
In the bowl of a stand mixer fitted with the paddle attachment, beat the butter and brown sugar on medium-high speed until light and fluffy, 2 to 3 minutes. Reduce the speed to medium-low, add the eggs one at a time, and beat until creamy, 1 to 2 minutes. Slowly add half the flour mixture, then the milk mixture, then the remaining flour mixture, beating until just blended after each addition. (The batter may appear slightly separated; this is okay.)
Divide the batter evenly*** among the liners and bake until the tops are puffy and dry to the touch and a toothpick inserted into the center comes out clean, 16 to 18 minutes****. Transfer the pan to a wire rack and cool completely.
While the cupcakes are cooling, in a heavy-bottomed skillet, toast the pecans** over medium-low heat, stirring frequently, for 7 to 8 minutes. Transfer to a plate to cool. Once cool, place in a food processor and process until the nuts are the size of large bread crumbs, 10 to 15 seconds. Frost the cupcakes with brown sugar frosting and arrange them on a baking sheet. Sprinkle the toasted pecan crumbs evenly over the cupcakes, gently pressing to adhere them to the frosting and letting excess pecan crumbs fall onto the baking sheet.
Notes
* I was able to make 16 cupcakes. ** I used candied pecan halves and did not toast them. *** About ⅔ full. ****My batch took 19 minutes.