Preheat the oven to 350 degrees. Grease an 8x8-inch glass baking dish with nonstick cooking spray.
In a large, microwave-safe mixing bowl, add the chopped baking chocolate, butter, and 1 cup of the chocolate chips. Microwave on high for 112 minutes. Whisk the melted butter into the melted chocolate.
Whisk the sugar, vanilla, flour, cocoa powder, and salt into the butter-chocolate mixture. Whisk the eggs and instant coffee granules into the batter. Whisk for about 1 minute, or until the batter is smooth. Fold in the remaining 1 cup chocolate chips and then stir in the caramel bits. Drop the sea salt all over the top of the batter, pinchful at a time.
Pour the batter into the greased baking dish. Bake in the preheated oven for 30 to 35 minutes until a toothpick inserted in the center comes out clean. Let cool slightly before cutting and serving.