Place the beans in a large bowl and cover with cold water, 2 inches above. Leave it out on the counter overnight.
Twelve hours later, drain the beans and transfer them to a large pot. Cover with cold water, add sea salt and bring to a boil. Reduce the heat to medium and simmer for 40 minutes or until tender.
Drain the beans and reserve the cooking liquid.
Transfer the drained beans back to the large pot and set aside.
Meanwhile when the beans are simmering, in a mixing bowl combine 1/2 cup molasses, brown sugar, prepared mustard, dry mustard, baking soda and black pepper; stir and set aside.
Take 1 slice of bacon and rub the sides of the inside of the bean pot. Cut bacon slices into pieces; set aside.
Place 4 onion pieces at the bottom of the pot and set aside.
Preheat oven to 325ºF
Pour the sauce over the beans and mix to coat. Add bacon pieces, stir and pour half of the bean mixture into the bean pot over the 4 onion pieces. Add the remaining onion pieces and pour in the remaining sauce. Season with more black pepper and add the remaining ¼ cup of molasses; stir just the top to spread the molasses evenly.
Pour in enough of the reserved liquid to cover the bean mixture.
Cover with the lid and transfer to the preheated oven; cook for 6 hours.
Every hour, check to see if it needs more liquid. If so, add more of the reserved liquid.
The last hour, pour in enough liquid to cover and continue cooking without the lid to darken the beans.