Rinse and sort beans in a large pot. For 2 cups of beans add 8 cups of hot water. Bring to a rapid boil and boil for 2 minutes. Remove from heat, cover and let stand for 1 hour. Drain and rinse beans.
Combine beans with diced onion, garlic and bay leaves in a large pot and cover with water by several inches. Add a generous pinch of salt. Bring to a boil, reduce to a simmer, and cook, topping up with water as necessary, until beans are fully tender, about 45-60 minutes.
Drain beans, reserving broth. Discard bay leaves. Pour beans into a Duch Oven.
Pour molasses into a 2-cup liquid measuring cup. Add sugar, mustard, a very generous dose of freshly ground black pepper, and a pinch of salt. Add 1 1/2 cups of broth to molasses mixture and stir until molasses is completely dissolved. Reserve remaining broth.
Preheat oven to 325°Saute bacon bits in a pan over medium-high heat, stirring occasionally, until lightly brown, about 4 minutes. Add to beans.
Add broth/molasses mixture and stir well to combine. Add enough reserved bean-cooking water to top beans, then stir once more, leveling out beans so that none are sticking up above the liquid level.
Place in oven and bake -uncovered- until beans are extremely tender but still mostly whole, with only a small fraction beginning to burst, about 4 hours. Check beans once or twice per hour during baking, adding remaining bean-cooking liquid (switching eventually to boiling water if you run ouas needed to prevent the beans on the surface from drying out. Stir beans twice during the baking process to submerge the top ones, leveling them out each time; over time, a dark, browned crust will form on the surface of the beans (this is good). The goal throughout is to keep the liquid level just high enough that the upper beans don't desiccate, but not so high that the surface doesn't brown. Stop adding liquid during the last hour of baking unless the level becomes perilously low.
Remove beans from oven and stir them very well. The sauce should form into a thickened, starchy glaze. If it's too dry, add boiling water sparingly until a glaze is achieved; if it's too wet, simmer briefly on the stovetop until reduced to desired consistency. Adjust seasoning with salt and pepper. If beans are too sweet for your taste, a small splash of cider vinegar can help balance the flavor (though I never thought my beans needed it).
Keep warm until ready to serve. Beans can be refrigerated for up to 1 week. Reheat in a saucepan, adding water gradually as needed to loosen them back up.