Place the potatoes on a baking sheet and cook the potatoes whole, do not pierce. Bake for 45 minutes to 1 hour. Lightly squeeze the potatoes - if they are soft, they are done. Let cool.
In a small saute pan over high heat, add the pecans and lightly toast. Add 4 tablespoons of butter, reduce the heat to medium, add the agave and spices, and allow to simmer for 4 to 5 minutes. Add the whiskey and continue to simmer for 5 minutes more.
Peel the potatoes and cut into 1/2-inch slices. Butter the bottom and sides of an 8 by 8-inch baking dish. Arrange the sweet potatoes, alternating with the apples. Pour the whiskey-pecan mixture over the top and place in the oven.
Bake for 30 minutes, basting the top with the whiskey sauce once at 15 minutes.