Preheat oven to 350 degrees. Line two muffin tins with paper liners. Grate pumpkin in a food processor or on the large holes of a box grater (you should have about 2 1/2 cups). Transfer to a medium bowl, and add pumpkin puree and pecans.
In the bowl of a food processor fitted with the metal blade, combine flour, sugar, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves; pulse to combine. With machine running, add oil and eggs; process until smooth, scraping sides of bowl as needed. Add pumpkin mixture; pulse to combine.
Spoon about 1/3 cup batter into each cupcake liner. Bake until a tester inserted in the center comes out clean, about 25 minutes. Transfer to a wire rack to cool.
Make the marzipan pumpkins: Tint two-thirds almond paste orange, adding food color a dab at a time until desired color is reached. Tint a quarter of remaining paste brown and the rest green. Shape into leaves, stems, and pumpkins (see instructions below).
Decorate cupcakes with frosting and marzipan pumpkins. Store in airtight containers at room temperature up to 2 days
Marzipan Pumpkin How-To: Using a small rolling pin, roll out green almond paste about 1/8 thick; use a leaf cutter to cut out leaf shapes. Roll brown into small ropes; cut and shape into stems. Using the palms of your hand, shape orange into three-quarter-inch globes. Use a toothpick to poke holes in tops of pumpkins and to press creases from top to bottom. Attach leaves and stems to tops with a bit of frosting.
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