In a makeshift double boiler over low heat, melt chocolate and butter, stirring occasionally. Remove pan from the heat and whisk in the cocoa. Set aside to cool slightly.

In the bowl of a stand mixer, beat together eggs and sugar on medium-high speed for 1 minute. Reduce speed to low and add vanilla and salt until combined, about 15 seconds. Keep mixer on low and slowly pour in chocolate mixture into the egg mixture (you can also stir it in by hand).

Remove bowl from mixer and stir in the flour with a wooden spoon until just combined. Stir in the chocolate chips and chopped pecans.

Pour the mixture into the prepared pan, spread into the corners and level with a rubber spatula. Bake 25 minutes, or until the top is shiny and the center is still dense. Brownies will continue to bake once removed from oven.

Cool on a wire rack to room temperature, about 2 hours. Use parchment paper to lift brownies out of the pan and place on a cutting board.

Use a spoon or liquid measuring cup to drizzle caramel over the cooled brownies. Sprinkle chopped pecans and chocolate chips on top. Garnish with flaky sea salt. Cut and serve.