Preheat the oven to 325. Line 12 muffins cups with paper liners. In a small bowl, whisk together the brown sugar, cinnamon, salt, and pecans. Add the melted butter and mix until combined. Set aside.
In a large bowl, whisk together the flour, baking powder, salt, and sugar. Cut in the butter using a pastry blender or two knives, until the mixture resembles coarse crumbs. In a small bowl or a measuring cup, whisk together the eggs, greek yogurt, and vanilla. Add the wet ingredients to the dry ingredients and mix until just combined.
Scoop one tablespoon of batter into each of the muffin cups. Sprinkle about a teaspoon of the streusel mixture over the batter, then top with remaining batter. Sprinkle the tops of the cupcakes with the remaining streusel. Bake 30-35 minutes, or until a toothpick inserted into the center of the cupcake comes out clean. Remove and let cool.
While the cupcakes are cooling, add the tablespoon of butter to a small skillet and cook over medium low heat until lightly browned and fragrant. (Watch carefully so that it does not burn.) Add the powdered sugar to a medium bowl and add the brown butter. Whisk to combine. Whisk in the vanilla and add milk until the glaze is a thick honey consistency. Drizzle over the cooled cupcakes.