Heat a large pot of water to boiling. Boil the cubed sweet potatoes for about 5 minutes, or until they are beginning to get tender, but are not cooked through. Drain and set aside.
While the potatoes are boiling, position a rack in the middle of the oven and preheat to 375 degrees. Line a 2 quart baking dish with parchment paper.
In a medium mixing bowl, toss the pre-boiled sweet potatoes, diced apples and red onion together with sea salt and freshly ground black pepper. Spread the food out evenly in the baking dish, and bake for 10 minutes.
While the sweet potatoes are baking, in a sauce pan over medium-low heat, whisk together the maple syrup, cinnamon, nutmeg and cayenne pepper until it begins to gently simmer. Add the whiskey and continue to gently simmer another 5 minutes until slightly reduced, whisking occasionally.
Remove the dish from the oven, and gently toss everything, bringing the food from the bottom to the top. Sprinkle the chopped pecans evenly over the top, then drizzle the maple-whiskey glaze evenly over the top.
Return to the oven and bake another 10-15 minutes, or until the apples and sweet potatoes are fork tender but not mushy.
Optional: If desired, toast about ½ cup of whole pecans in a dry pan over medium heat for about 5 minutes or until crispy for garnish.