Combine beans in a large bowl with enough water to cover by 1 inch. Soak overnight.

Drain beans the next day and place in a pot with 1 quart fresh water and kombu. Bring to a boil, cover, and simmer 30 minutes. Drain beans.

Place onion in a food processor and puree. Spread puree into the bottom of a slow cooker insert. Add drained beans and enough fresh water to cover.

Mix vinegar, dry mustard, ketchup, molasses, brown sugar, and black pepper together in a bowl and stir this mixture into the slow cooker. Cover top with aluminum foil and slow cooker lid.

Cook on Low for 4 hours. During cooking, check every 1 to 2 hours to ensure beans are covered with water; add hot water as needed. At 4 hours, transfer 1 cup beans to a bowl and mash. Return mashed beans to the slow cooker. Continue to cook another 6 hours.

Stir in liquid smoke before serving.