In a large mixing bowl (or the bowl of a stand mixer), combine the warm water, dark molasses, and instant dry yeast. Stir gently and let sit for 5-10 minutes, until the mixture becomes foamy, indicating the yeast is active.

In a separate large bowl, whisk together the dark rye flour, bread flour, unsweetened cocoa powder, kosher salt, caraway seeds (if using), and instant coffee powder (if using). Ensure all ingredients are well combined.

Add the dry ingredient mixture to the wet yeast mixture. Mix with a sturdy wooden spoon or the dough hook of a stand mixer on low speed until a shaggy, cohesive dough forms. Make sure there are no dry pockets of flour.

Turn the dough out onto a lightly floured surface or continue kneading with the stand mixer's dough hook on medium-low speed. Knead for 8-10 minutes until the dough becomes smoother, more elastic, and slightly tacky. Pumpernickel dough will be denser and less elastic than a typical white bread dough.

Lightly grease a clean large bowl with vegetable oil or butter. Place the kneaded dough in the bowl, turning it once to coat all sides with oil. Cover the bowl tightly with plastic wrap or a damp kitchen towel. Let the dough rise in a warm, draft-free place for 1.5 to 2 hours, or until it has roughly doubled in size. This rise may be slower than for white bread.

Gently punch down the risen dough to release the air. Turn it out onto a lightly floured surface. Shape the dough into a tight, even log, tucking the ends underneath to create a smooth top. Grease a 9x5-inch loaf pan with vegetable oil or butter and dust lightly with cornmeal to prevent sticking. Place the shaped dough into the prepared loaf pan.

Loosely cover the loaf pan with plastic wrap or a damp kitchen towel. Let the dough rise again in a warm place for another 45-60 minutes, or until it has risen about 1 inch (2.5 cm) above the rim of the pan. It should look noticeably puffy.

About 20 minutes before the second rise is complete, preheat your oven to 375°F (190°C).

Once the loaf has finished its second rise, place the loaf pan in the preheated oven. Bake for 30 minutes. Then, reduce the oven temperature to 350°F (175°C) and continue baking for another 30-35 minutes, or until the internal temperature of the bread reaches 200-210°F (93-99°C) when measured with an instant-read thermometer. The crust should be dark and firm to the touch. If it starts to brown too quickly, you can loosely tent it with aluminum foil.

Carefully remove the bread from the oven. Immediately turn the loaf out of the pan onto a wire rack to cool completely. This is crucial for pumpernickel bread; allow it to cool for at least 2-3 hours before slicing. Slicing too early can result in a gummy texture due to the high rye content.