I'm going to go in a little different direction here. From what I saw you weren't doing anything to irritate your W. She "perceived" that she was irritated by you. But guess what? You're not her monkey who is there to make her happy. If SHE feels uncomfortable, I would have told her, that she is more than welcome to find another place.
If she threatened to take the kids, then firmly say no because SHE is the one who feel uncomfortable about the home and not them. That you are willing to work on things to make her feel comfortable, but she does not have the right to blame her unhappiness on you and then go off as if you didn't have a care in the world.
Again I'll reiterate...it is not your job to make her happy. It's obvious she's making herself unhappy. That doesn't affect you. Start by setting what YOU want to happen and not just reacting off of what she wants.
