Preheat oven to 350ºF. Line a 12-cup muffin pan and 4 cups of a 6-cup muffin pan with paper baking cups; lightly mist with cooking spray.
Stir together almond flour, coconut flour, cinnamon, ginger, baking powder, salt, baking soda, and ground cloves in a large bowl until combined. Whisk eggs in a separate bowl. Add pumpkin, coconut oil, molasses, syrup, and vanilla to eggs and whisk until combined. Add flour mixture to egg mixture and stir until incorporated. Fold in walnuts, cranberries, or chocolate chips, if desired.
Divide batter among muffin cups, filling them two-thirds full. Bake until cooked through, 28 to 35 minutes. Let cool in pans for about 5 minutes. Remove from pans and place on a wire rack to cool completely. Wrap leftover muffins in plastic and refrigerate for up to 5 days.