I think you should tell your husband to stop yelling, and make a big point of letting the boy know he loves him and is proud of him.
Boys who felt their father's love and pride have such an advantage over boys who are scorned by their dads. You've known that your son has "always" thought his dad doesn't love him - make him quit it.
I know how you feel. We have an 11 yr. old daughter that always questions our love, especially when she's in trouble. Usually it ends with her telling us she hates me, so I usually reply, "then I guess I'm doing my job". It never lasts long. When she gets over being angry sometimes she will try manipulating one or both of us, but we stand firm. Our daughter had complicated behavioral issues since @ 2, we've since put her through BioFeedback through The Drake Institute, I'm not sure if you've heard of it, I'm in California and not sure where you are located. But they really pushed Positive Motivation, it really does work when YOU and THEY really apply themselves. Sometimes, though, I strongly believe in a good kick in the pants. They need boundries. Good Luck.