To be honest, I think things would get a whole lot better if son and his new wife moved out of your home and got their own place.
From what I've read here, as other people have said, neither of you come out smelling like a rose.
If they continue to stay with you, though, there is no way any relationship is going to get better. You have building resentment, and so does your DIL.
Time for them to be married and on their own, and on their own insurance. If they aren't paying you any rent, and they are working - they should certainly be able to afford an apartment.