Prepare Crust: Pulse pecans in a food processor 10 to 12 times or until finely chopped. Transfer pecans to a small bowl. Pulse 1 1/4 cups flour and 2 Tbsp. granulated sugar in processor 2 or 3 times to combine. Add 1/2-inch butter pieces, and pulse 10 to 12 times or until mixture resembles coarse meal. Add pecans, and pulse 2 or 3 times to combine. With processor running, pour 2 Tbsp. ice-cold water and 1 tsp. vanilla through food chute, and process just until dough comes together. Transfer dough to a lightly floured surface, and shape into a disk. Wrap disk in plastic wrap, and chill 30 minutes.
Preheat oven to 350°. Place dough disk between 2 sheets of lightly floured wax paper, and roll to a 12-inch circle. Fit piecrust into a 9-inch deep-dish pie plate; fold edges under, and crimp. Prick bottom and sides of dough with a fork; line dough with parchment paper, and fill with pie weights or dried beans.
Bake at 350° for 20 minutes. Remove weights and parchment paper, and bake 10 to 12 more minutes or until browned. Cool completely on a wire rack (about 1 hour).
Prepare Filling: Whisk together brown sugar and next 2 ingredients in a medium saucepan. Gradually whisk in milk. Cook over medium heat, whisking constantly, 8 to 9 minutes or until mixture is smooth and begins to thicken.
Gradually whisk about one-fourth of hot sugar mixture into egg yolks; gradually whisk egg yolk mixture into hot sugar mixture, and cook, whisking constantly, 2 to 3 more minutes or until mixture is thick and smooth and just begins to bubble. Remove from heat, and whisk in 1-inch butter pieces and 2 tsp. vanilla. Pour filling into prepared piecrust.
Prepare Meringue: Beat egg whites and next 2 ingredients at high speed with an electric mixer until foamy. Gradually add 6 Tbsp. granulated sugar, 1 Tbsp. at a time, beating until stiff peaks form and sugar dissolves. Spread meringue over hot filling, sealing edges.
Bake at 350° for 10 to 12 minutes or until golden brown. Remove from oven to a wire rack, and cool completely (about 2 hours). Chill 4 to 6 hours before serving.