This is a classic case of fear aggression. I'm glad she is willing to work with a trainer. These behaviors will take time to rehabilitate - she has destroyed any trust he may have had in her - and that will take time to overcome. She needs to be aware that every single time she raises her voice, and especially if she hits him, it reinforces his fear and will take just that much longer to undo the damage.
Methods to stop the bad behaviors would depend on the behavior. If she doesn't catch him in the act of peeing, then she cannot correct him at all. I'm actually surprised that she isn't finding spots where he has hidden to pee. Normally a dog that has learned to associate his own waste with his human suddenly becoming violent will learn to hide his waste - in his mind it's not WHERE he went, but that his human saw it so he will make every effort to make sure they don't see it. If she does catch him in the act, a simple "NO" (said firmly, but calmly) while moving him outside will do. Once outside, if he finishes the act, then praise like he just won the lottery for you. And the spots must be cleaned with an enzyme solution to destroy the smell. If the smell is still there, he'll continue to go there. Most of the destructive behaviors are likely frustration and anxiety. I would not advocate for use of the crate since it's been used as a punishment for him. Increase the exercise, confine him in an area of the house where he cannot damage anything (and that can be easily cleaned if he has an accident) when he needs to be confined, use the umbilical training when she is home and he is not confined, practice NILF (nothing in life is free) and definitely work with the trainer.
Livin in a Newfie Drool Zone