Make the cupcakes: Preheat the oven to 350 degrees F and line a muffin pan with 12 cupcake liners. Whisk the flour, baking powder and salt in a medium bowl.
Beat the eggs and granulated sugar in a large bowl with a mixer on medium-high speed until pale and fluffy, about 2 minutes. Reduce the speed to medium low; slowly beat in the melted butter, then add the orange zest and vanilla.
Beat in the flour mixture in 2 additions, alternating with the milk, beginning and ending with the flour mixture; beat until just combined (do not overmix).
Divide the batter evenly among the muffin cups, filling each about two-thirds of the way. Bake until a toothpick inserted into the centers comes out clean, about 18 minutes. Let cool 5 minutes, then remove the cupcakes to a rack to cool completely.
Meanwhile, make the frosting: Bring the orange juice to a boil in a saucepan; reduce the heat to medium and simmer until reduced to1 1/2 tablespoons, about 8 minutes. Let cool.
Beat the cream cheese in a large bowl with a mixer on medium-high speed until smooth and fluffy. Beat in the butter, a little at a time, until smooth. Reduce the mixer speed to low; sift the confectioners' sugar into the bowl and beat until smooth. Add the vanilla, the cooled orange syrup, orange zest and food coloring and beat on medium speed until combined. Refrigerate until spreadable, about 15 minutes. Spread the frosting on the cupcakes; top with candied orange zest.