Preheat oven to 425 degrees Fahrenheit. Line cupcake pan with paper cups. Mix the flour, sugar, baking powder, baking soda, cinnamon, nutmeg and salt in one bowl.
Whisk the eggs in another bowl. Then slowly whisk in the oil, sour cream and vanilla. Whisk this mixture into the bowl of dry ingredients. Add the coconut and shredded carrots. Whisk until combined.
Fill paper cups ⅔ full. Bake for 15 to 17 minutes or until the center is baked. Test doneness with a toothpick (will come out clean) or press lightly in the center with your finger, if the cake springs back, it's done. Allow cupcakes to cool.
Make frosting by beating the cream cheese and butter in a bowl with a hand mixer. Add orange zest, orange juice, and powdered sugar all at once. Beat until just combined. Prepare a piping bag and tip. Fill it with frosting and pipe frosting onto each cupcake. Sprinkle the tops with extra zest for a garnish. Store cupcakes in an airtight container.