I haven't read all of this, so some one may have answered: the sugar and the tomatoes don't let them soften, and will actually make even soft cooked beans tougher. Add the sugar and/or tomatoes at the very end. As for gas, to 2 quarts of cooked beans, add a 15 ounce can of crushed pineapple. doesn't change the flavor, but eliminates the gas. Also, when I'm cooking beans, I cover them with cold water, bring to a boil, you can even let them sit overnight at this point, then drain and rinse the beans very well, cover with cold water again and simmer until soft. discarding the soaking water also reduces the gas.
Old beans take longer to cook, but even 20 year beans I have cooked to softness, soak them overnight first, without seasoning.