Preheat oven to 350 degrees F (175 degrees C). Prepare cupcake pans with paper liners.
Combine cake mix, pumpkin, applesauce, 1 teaspoon ground cinnamon, 1/2 teaspoon ground nutmeg, 1/2 teaspoon ground ginger, 1/4 teaspoon ground cloves, and 1/4 teaspoon ground allspice in a large bowl. Using electric mixer, combine until thick cake batter forms.
Portion into prepared cupcake tins, about 2 tablespoons each. Bake for 15-20 minutes until toothpick comes out clean and the tops begin to brown.
For the Frosting: With an electric mixer fitted with a whisk attachment, whip cream cheese and butter until well combined, scraping sides of the bowl as necessary. Add vanilla and whip until incorporated.
Add 3 cups of powdered sugar, one cup at a time, whipping the frosting to incorporate each cup fully before adding the next. Add the vanilla seeds and whip one last time. Spread or pipe onto cupcakes.
For the Candy: Line a baking sheet with aluminum foil. Sprinkle with powdered sugar and pecan pieces, if desired.
Combine sugar, water, Mott's(R) Natural Applesauce, cinnamon, and nutmeg to a large saucepan. Heat on medium until mixture starts to boil. Stir regularly until candy reaches hard-crack phase (300 degrees F on a candy thermometer, or until the candy audibly crackles when dropped into a cup of cold water).
Pour prepared candy over powdered sugar and pecan pieces. Allow to completely cool and harden before breaking into pieces. Sprinkle onto frosted cupcakes.