In a large bowl, combine brown sugar and flour. Beat in the sweet potatoes, milk, butter, eggs, nutmeg and salt. Pour into pastry shell. Bake at 350° for 55-60 minutes or until a knife inserted in the center comes out clean. Cool on a wire rack.
For topping, in a small heavy skillet, melt butter. Add pecans; cook over medium heat until toasted, about 4 minutes. Sprinkle with sugar. Cook and stir for 2-4 minutes or until sugar is melted. Sprinkle over pie. Refrigerate leftovers.