Make the cupcakes: Preheat the oven to 350 degrees F and line a 12-cup muffin pan with paper liners. Whisk the flour, baking powder, baking soda and salt in a bowl until combined. Whisk the eggs, granulated sugar, milk, vegetable oil, lemon zest, lemon juice and vanilla in a large bowl until combined. Whisk the flour mixture into the egg mixture.
Divide the batter evenly among the prepared muffin cups, filling them to just below the rim. Bake until a toothpick inserted into the center of a cupcake comes out clean, 25 to 30 minutes. Let cool 15 minutes in the pan, then transfer to a rack to cool completely.
Make the meringue: Beat the egg whites and salt in a large bowl with a mixer on medium speed until foamy, about 1 minute. Increase the mixer speed to high and gradually beat in 2 tablespoons granulated sugar; beat until stiff shiny peaks form, about 3 minutes.
Combine the remaining 6 tablespoons granulated sugar, the corn syrup and 1/4 cup water in a saucepan over medium-high heat. Cook until the mixture registers 245 degrees F on a candy thermometer, about 6 minutes; remove from the heat. With the mixer on medium speed, slowly pour the hot sugar syrup into the egg whites; increase the speed to high and beat until the meringue is fluffy and cool, about 6 minutes. Beat in the vanilla. Transfer the meringue to a pastry bag fitted with a large round tip and pipe onto the cupcakes; set aside at room temperature to firm up, about 15 minutes.
Meanwhile, make the glaze: Whisk the confectioners' sugar, lemon juice, limoncello and food coloring in a microwave-safe bowl until smooth. Microwave 1 minute, then whisk again until the sugar dissolves; let cool about 5 minutes, stirring occasionally. Dip the meringue-covered tops of the cupcakes into the glaze, letting the excess drip off. If the glaze gets too thick, microwave 20 seconds.