Lemon Pecan Pie

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1 cup firmly packed dark brown sugar

1/2 cup granulated sugar 

2 large eggs 

1/2 cup (1 stick) unsalted butter, melted 

1 1/2 teaspoons vanilla extract 

2 teaspoons finely grated lemon zest plus 3 tablespoons juice 

2 tablespoons milk 

2 tablespoons all-purpose flour 

1 cup chopped pecans plus 1 cup pecan halves 

One store-bought 9-inch deep-dish pie shell, unbaked