Preheat oven to 400 degrees. Roll out pastry and line pie pan. Prick dough with fork, then line with foil. Fill bottom with pastry weights or dry beans. Bake 8 minutes, remove foil and weights, and bake 8-10 minutes longer, until pastry looks dry and is barely starting to color. Remove from oven and let cool.
Place flour, 1/4 cup brown sugar, granulated sugar, 1/2 t. cinnamon, and 1/2 t. salt in food processor and process briefly to blend. Dice 6 T. butter and add, along with pecans; pulse until mixture resembles breadcrumbs. Set aside. Increase oven temperature to 450 degrees.
Melt remaining 3 T. butter in a large skillet. Add apple slices and saute over medium heat about 5 minutes, until a bit softened around the edges, with some just starting to brown. Remove from heat. Mix remaining 1/2 cup brown sugar, 1/2 t. cinnamon, and a pinch of salt, along with the cloves and nutmeg. Pour over apples and fold together. Fold in whiskey.
Pour contents of skillet into crust and top with crumbs. Place pan on a baking sheet, bake 10 minutes, lower heat to 350 degrees and bake about 40 minutes longer, until topping browns and juices bubble. Allow pie to cool completely before cutting. Pie can be made a day in advance and warmed for serving.