Make the cupcakes: Preheat the oven to 400°F. Line two 12-cup muffin tins with paper liners.
Grind the Mexican chocolate into a fine powder using a molcajete (a mortar and pestle) or by placing the tablet in a plastic bag and crushing it on a thick wooden cutting board with a mallet. Combine chocolate powder in a bowl with cocoa powder, flour, sugar, baking powder, baking soda, cinnamon, salt, and chocolate chips.
In another bowl, beat milk, eggs, oil, and vanilla until smooth. Add milk mixture to chocolate mixture and stir until blended. Spoon batter into muffin cups so that cups are half full. Bake for 12 minutes, or until a toothpick inserted in the center of a cupcake comes out clean. Allow cooling in pan before frosting.
Make the frosting: Combine confectioners' sugar, butter, lemon zest, lemon juice, vanilla, salt, and food coloring in a bowl. Beat with an electric mixer until well mixed, fluffy, and smooth. Place frosting in a pastry bag with a petal tip or in a plastic bag with a small notch cut out of one corner. Since marigolds are round and have many petals, pipe several petal shapes together in a circle on top of each cupcake.