Preheat oven to 375 degrees and line a muffin pan with paper cupcake liners.
In a medium bowl, whisk together the flour, baking soda, baking powder, cinnamon, and salt. Set aside.
In large bowl, whisk the eggs, oil, and sugar together, about 3 minutes.
Stir in shredded carrots, crushed pineapple, coconut flakes, and pecans pieces.
Add in the flour mixture gradually to the wet ingredients, combining after each addition.
Fill the muffin cups about ⅔ of the way full.
Bake for 22 - 26 minutes. Test with a toothpick - it should come out clean with very little crumb on it. Remove from oven and cool completely on a wire rack before frosting.
While the cupcakes are baking, make the candy carrots: melt the candy wafers according to the package directons for the microwave. Line a baking sheet with parchment papers.
Fill one piping bag with the orange melted chocolate and one with the green. Pipe squiggly lines for the carrots and then do the same with the green for the tops. Allow to set before placing on frosted cupcakes. Add sprinkles to some of the cupcakes and some with the candy toppers.