Make the cupcakes: Preheat the oven to 350 degrees F and line a muffin pan with 12 cupcake liners. Combine the flour and almonds in a food processor and pulse until the almonds are finely ground, about 1 minute. Add the baking powder, baking soda and salt and pulse to combine.
Whisk the eggs, sugar, buttermilk, vegetable oil and lemon zest and juice in a large bowl. Add the flour mixture and whisk until just combined. Divide the batter among the muffin cups, filling them three-quarters of the way. Bake until a toothpick inserted into the centers comes out clean, 16 to 18 minutes. Let cool in the pan 5 minutes; remove to a rack to cool completely.
Make the frosting: Combine 2/3 cup sugar and 1/4 cup water in a small saucepan; cook over medium-high heat until a candy thermometer registers 240 degrees F, about 12 minutes. Beat the egg whites in a large bowl with a mixer on medium speed until foamy; increase the speed to medium high and beat until soft peaks form, 2 minutes. Sprinkle in the remaining 1/4 cup sugar and beat until stiff peaks form, 3 minutes. With the mixer running, slowly pour in the sugar syrup and beat until cool and glossy, 8 to 10 minutes.
Add the butter a little at a time, beating until incorporated. (It's OK if the mixture looks curdled at first; continue beating.) Beat in the food coloring, then add the lemon zest and juice and beat until smooth, 2 more minutes.
Make the candied zest: Remove the lemon zest with a vegetable peeler and slice into thin strands. Place in a small saucepan, cover with water and bring to a simmer over high heat. Drain the zest and return it to the saucepan; cover with water and repeat 2 more times. Bring the sugar and 3/4 cup water to a bare simmer in a separate saucepan, stirring until the sugar dissolves. Add the lemon zest strands and cook over low heat, 20 minutes. Drain the zest and arrange in clusters on a parchment-lined baking sheet; let dry.
Frost the cupcakes and top with the candied lemon zest.