Place the beans in a large container and cover by 2 inches of water. Soak until the beans are pale yellow and split apart easily when rubbed between your fingertips, about 12 to 18 hours.

Drain and rinse the beans. Working in three batches, process the soaked soybeans with the water in a blender until mostly smooth, about 3 minutes per batch, then transfer the mixture to a large Dutch oven.

Bring the soybean mixture to a boil over medium-high heat. Stir often with a rubber spatula to prevent scorching on the bottom or boiling over. Reduce the heat to medium-low and simmer until the liquid has slightly thickened, about 10 minutes.

Line a colander with butter muslin or a triple layer of cheesecloth and set it over a large bowl. Carefully pour the hot soybean mixture into the colander. Pull the edges of the muslin together to form a tight pouch and firmly squeeze with tongs to extract as much soy milk as possible; you should have about 8 cups of milk.

Transfer the strained soy milk to a clean Dutch oven and bring it back to a boil over medium-high heat, stirring frequently. Once it reaches a boil, remove the pot from the heat immediately. Stir the nigari and water together in a small measuring cup.

Stir the soy milk in a fast figure-eight motion with a rubber spatula and pour in half of the nigari mixture. Cover the pot and let it sit undisturbed for 2 minutes. Uncover and sprinkle the remaining nigari mixture over the surface, then stir gently using the same figure-eight motion about 6 times. Cover and let sit until clear yellow whey pools around the white curds, about 20 minutes.

Line a tofu mold with muslin and place it in a colander over a bowl. Use a slotted spoon to gently transfer the curds into the mold, taking care not to break them up. Fold the excess muslin over the top, add the press lid, and weight it with a 2-pound weight. Press until the desired firmness is reached: 20 minutes for soft, 30 for medium, or up to 50 minutes for firm.

Gently remove the tofu from the mold and place it in a baking dish filled with cold water. Let it sit for 10 minutes to fully set the texture. Serve fresh or store in an airtight container submerged in water for up to one week.