Combine 1 cup sugar, 1/2 cup pecans, and flour in a heavy saucepan; stir well.
Combine egg yolks and milk in a mixing bowl; mix well.
Gradually add milk mixture to pecan mixture, stirring until well blended. Cook over medium heat, stirring constantly, until mixture thickens and comes to a boil. Cook 1 minute, stirring constantly. Remove from heat; add butter and 2 teaspoons vanilla, stirring until butter melts. Pour into pastry shell.
Beat egg whites (at room temperature) until foamy. Add 1/4 cup sugar, 1 tablespoon at a time, beating until stiff peaks form. Beat in 1/4 teaspoon vanilla. Spread meringue over filling; seal to edge of pastry. Sprinkle with pecans. Bake at 400° for 10 minutes or until golden brown. Cool.