Make the cupcakes: Preheat the oven to 350 degrees F. Line a 24-cup mini-muffin pan with paper liners. Whisk the flour, baking powder and salt in a medium bowl. Beat the butter and granulated sugar in a large bowl with a mixer on medium-high speed until fluffy, about 4 minutes. Beat in the lemon zest. Beat in the whole egg, then the yolk, beating well after each addition; beat in the vanilla. Reduce the speed to low and beat in the flour mixture in three batches, alternating with the milk. Beat on medium speed until combined.
Divide the batter among the mini-muffin cups, filling them two-thirds of the way. Bake until the cupcakes are golden and the tops spring back when pressed, about 15 minutes. Transfer to a rack and let cool 10 minutes, then remove the cupcakes to the rack to cool completely.
Meanwhile, make the frosting: Beat the butter, confectioners' sugar and salt in a large bowl with a mixer on medium speed until combined. Add the vanilla and beat on medium-high speed until creamy, about 3 minutes. Add the milk and beat until fluffy, about 1 more minute.
Divide the frosting among 3 small bowls. Tint one yellow, one pink and one blue with food coloring. Drop alternating spoonfuls of the frosting into a pastry bag fitted with a 1/2-inch round tip. Pipe the frosting in a swirl onto the cupcakes. Serve in a clean egg carton.