Drain the beans. In a large, heavy, ovenproof pot, combine the beans and stock/water. Place the pot over medium-high heat and bring to a boil. Lower the heat to a simmer and cook until the skin of the beans crinkle/curl up when you blow on them.
Preheat the oven to 350°F. Adjust the racks in your oven to make room for the pot.
In a medium bowl, whisk together the molasses, apple cider vinegar, miso, tamari, mustard, garlic, paprika, and ginger. Add this mixture to the beans, and bring the pot back up to a boil.
Cover the beans and place the pot in the oven. Cook the beans until very tender and the liquid has thickened slightly (it will continue to thicken). It’s important to stir and check the beans every 30 minutes. They should take about 1 ½ hours total. Season the beans with salt and more vinegar if you wish, and serve hot.