Bring beans and 3 quarts hot water to a boil; continue to boil for 2 minutes. Let sit at least 1 hour, but it is best to allow beans to soak in the pot overnight.
Cook the bacon for 5 minutes in a 3 to 4-quart pot. Add onion, garlic and ginger, and cook for an additional 5 minutes. Add drained beans and next 10 ingredients (molasses through allspice). Bring to a simmer. Add salt and pepper and mix well. Cover with remaining bacon. Bake in a 300-degree oven for 5 to 6 hours or until beans are very tender. If necessary, add additional cider during cooking to keep beans covered.
When cooked, remove thyme sprigs and bay leaves, correct seasonings and serve.