Preheat the oven to 350 degrees F (175 degrees C). Lightly grease a 9x13-inch baking dish.

Combine bread cubes, apples, and raisins in a very large bowl.

Whisk eggs, brown sugar, vanilla extract, cinnamon, allspice, nutmeg, and salt together in another large bowl until well combined. Whisk in milk and apple cider. Pour mixture over bread mixture, and toss gently using a spatula until evenly coated. Let bread pudding mixture stand for 15 minutes.

Pour bread pudding mixture into the prepared pan and smooth into an even layer.

Bake in the preheated oven until puffed and lightly browned and a knife inserted in the center comes out clean, about 45 minutes.

Remove from the oven and reduce the oven temperature to 325 degrees F (165 degrees C). Let bread pudding cool for at least 15 minutes; pudding will sink slightly.

Meanwhile, spread pecans on a baking sheet. Bake in the hot oven until lightly browned, about 5 minutes, watching carefully to prevent burning. Remove from the oven and set aside.

Combine brown sugar, corn syrup, heavy cream, and butter in a large, heavy saucepan. Bring to a boil over medium heat. Reduce heat to medium-low and continue cooking, stirring constantly to prevent burning, until mixture is reduced to 3 cups, 10 to 15 minutes. Remove sauce from heat. Stir in pecans, bourbon, and vanilla extract.

Serve sauce with bread pudding.