Preheat oven to 350 degrees F (175 degrees C). Grease and flour a fluted tube pan.
Mix 3 cups all-purpose flour, white sugar, baking soda, cinnamon, allspice, salt, cloves, and nutmeg together in a bowl.
Beat eggs in a separate large bowl; add vegetable oil, buttermilk, and 1 tablespoon vanilla. Beat until smooth. Pour egg mixture into flour mixture; stir together with a large spoon. Fold apples and pecans into batter. Pour batter into the prepared pan.
Bake in the preheated oven until a knife inserted in the center of the cake comes out clean, 60 to 75 minutes. Cool cake in pan.
Cook and stir margarine and brown sugar together in a saucepan over medium heat until sugar is dissolved, about 5 minutes. Add 2 tablespoons flour; stir constantly until combined. Stir in milk and 1 tablespoon vanilla. Cook and stir until thickened, 5 minutes.
Invert cake onto a plastic cake carrier or container; poke holes over entire cake using a knife. Pour hot icing over entire cake. Pour any remaining icing into the center of the cake. The icing will absorb into the cake overnight.