Preheat oven to 350°. Line a 12-cup muffin pan with paper liners.
In a large bowl, whisk together flour, baking soda, cinnamon, ginger, and salt.
In a medium bowl, whisk together brown sugar, orange zest and juice, oil, eggs, and vanilla; stir in carrot and apple. Stir sugar mixture into flour mixture just until dry ingredients are moistened. Stir in raisins and pecans. Divide batter among prepared muffin cups. Top each with an orange slice (if using); sprinkle with granulated sugar.
Bake until a wooden pick inserted in center comes out clean, 20 to 25 minutes. Let cool in pan for 5 minutes. Remove from pan, and let cool completely on a wire rack. Store in an airtight container for up to 2 days.
Recipe by Paula Deen Magazine at https://pauladeenmagazine.com/sunrise-muffins/