Bring the sugar, water, and vanilla extract to a boil in a medium frying pan. Reduce heat to low and add the blood orange slices in a single layer. Allow to cook in the syrup for 40 minutes, turning them halfway through. Remove them from the syrup and allow to cool on a wire rack, then cut them into quarters.
Preheat the oven to 350 degrees Fahrenheit and line a muffin tin with cupcake liners. Melt the butter in a medium stainless steel or white enameled saucepan over medium low heat. Continue cooking it until the butter smells nutty and toasty and turns deep gold in color, then remove it from the heat and allow to cool for 5 minutes.
Sift the flour, cocoa powder, and baking powder into the bowl of a stand mixer. Add the sugar and salt and mix at low speed with the paddle attachment to combine. Add the brown butter, water, and egg and beat at low speed until smooth. Add the creme fraiche, whole milk, vanilla extract, and blood orange zest and mix at low speed until just combined.
Evenly distribute the batter between the cupcake liners, filling them about 3/4 full. Place the pan in the oven and bake for about 25 minutes or until a toothpick inserted into the center of each one comes out clean. Remove the lined cupcakes from the pan and let them cool completely on a wire rack.
In the top of a double boiler over gently simmering water, whisk together the egg, egg yolk, granulated sugar, 3 tablespoons of the blood orange juice, and the butter. Continue whisking until the mixture has noticeably thickened, about 10-15 minutes. Remove from heat, whisk in the remaining 2 teaspoons of blood orange juice and place the top of the double boiler in an ice bath to help the curd cool as you whisk it until cooled to room temperature. Cover and place in the refrigerator.
Heat the cream in the top of a double boiler until warm, add the chocolate chips and stir until the chocolate has melted and the mixture is smooth. Remove from heat and allow the ganache to cool to room temperature before transferring the ganache to the bowl of a stand mixer fitted with the paddle attachment and beating at medium high speed until smooth and slightly fluffy, about 2 minutes.
Scoop 1 tablespoon out of the tops of each of the cupcakes and fill the holes with 2 teaspoons of the blood orange curd. Top with the chocolate ganache and a quarter slice of the candied blood oranges and serve.