Preheat oven to 350°F and line muffin tin with paper liners.
In a large bowl whisk together the flour, sugar, baking soda, baking powder, and salt until combined; set aside.
In another large bowl combine the cocoa and the hot water; add the eggs, buttermilk, oil and vanilla and beat until combined.
Add the dry ingredients into the wet ingredients and mix until smooth.
Scoop batter into prepared pans and bake for 20-22 minutes or until tops spring back when touched; remove from pans and allow to cool completely before frosting.
In a standing mixer fitted with a paddle, mix together sugar and butter. Mix on low speed for 2 minutes then increase speed to medium and beat for another 3 minutes. Pour in vanilla, milk, and caramel. If needed, adjust frosting to a pipeable consistency, if the frosting is too stiff and milk. If the frosting is to loose add powdered sugar.
Using the end (handle) of a cooking spoon. Place a hole going halfway down the center of each cupcake. Dip end/handle in water every 3 cupcakes.
Fill these holes with caramel to the top. Sprinkle lightly with sea salt.
Place a star tip in your piping bag. Fill piping bag with frosting. Frost each cupcake with a Gigi's swirl, creating 3 layers of frosting.
Place cupcakes in the freezer for 15-20 minutes. Mix the semi sweet chocolate chips and the heavy cream in a double boiler. Stir constantly until all the chocolate chips are melted. Pour the ganache into a narrow container, and dip the cold cupcakes to cover 1/3 of the frosting. Bring the cupcakes to room temperature. Sprinkle each cupcake with sea salt.