Place the soaked beans in a large pot and cover with water to cover beans by about 2 inches.
Bring the pot to a boil, then reduce the heat to simmer the beans. Add water as needed to keep the beans covered.
Gently simmer beans until tender but not mushy. This should take between 45 minutes and 1 hour.
Preheat oven to 325°F.
While the beans cook, saute the bacon for about 10 minutes until it browns. Add the minced garlic and chopped onions and saute for 10 more minutes, until onions are translucent.
Mix tomato sauce, maple syrup, brown sugar, molasses, Worcestershire sauce, salt, pepper, smoked paprika, and dry mustard.
Once beans are pre-cooked, drain and reserve the cooking liquid.
Add the beans to a large, oven-safe casserole or a Dutch oven with a lid. Aluminum foil can be used instead of a lid.
Stir in the tomato sauce mixture, the bacon mixture, and enough reserved bean cooking liquid to cover the beans by 1/4 - 1/2 inch, depending on how saucy you like your beans.
Put beans in the preheated oven and bake for 3-4 hours, occasionally checking to ensure that liquid covers the beans. If you don't see liquid just covering the beans, add a little of the reserved cooking liquid until it does. Beans are finished when beans are finished. There is wide variability in beans, so it is important to check them often to ensure some sauce is still on top of them.
You can remove the lid or foil for the last 20-30 minutes to help thicken the sauce if needed.
Remove from oven and serve immediately or let cool. These baked beans can be reheated easily on the stovetop.