Sort through beans and pick out any stones, small and shriveled, excessively dirty, or otherwise look bad.
Pour beans into a large colander and rinse well. Pour rinsed beans into a 6-qt. slow cooker and cover with water by 2 inches. Place cover on and leave slow cooker OFF. Allow beans to soak overnight (about 8 - 12 hours).
Drain the soaked beans and rinse the slow cooker. Place onions, garlic and bacon into the slow cooker. Then add beans back into the pot. Add water, molasses, brown sugar, ketchup, chili pepper, vinegar, and pepper. (Salt will be added at the end.)
Cook on high for 10-12 hours until beans are tender. Add salt to taste, recommended full tablespoon.