For the cookies: Adjust oven racks to upper-middle and lower-middle positions and heat oven to 350 degrees. Line 2 standard 12-cup muffin tins with liners.
In a medium saucepan over low heat, melt butter. Remove from heat and whisk in brown sugar, eggs, and vanilla until smooth. Add flour, baking powder, salt and pecans and stir until combined. Scoop 2 tablespoons of mixture into each muffin cup. Bake, rotating tins from front to back and top to bottom halfway through baking, until golden brown, 15 to 18 minutes.
While cookies are baking, make the filling. Melt butter in small saucepan over medium-low heat. Stir in milk, granulated sugar, brown sugar, and crumbs and cook, stirring constantly, until thickened, about 5 minutes. Remove from heat and cover to keep warm until cookies come out of from oven.
For the topping: Remove cookies from oven and immediately sprinkle tops with chocolate chips. Working quickly, top each cookie with a heaping tablespoon of filling and sprinkle with chopped pecans. Cool completely on cooling rack, about 30 minutes. Remove cookies from tins.