S.H.
Your situation sounds fairly traumatic - and I will give you what little advice I have, but first know that God is bigger than any problem you are facing and his solutions are always the best.
That being said, I also live with my MIL and even though she is kind and respectful (to my face), I still struggle with negative feelings every now and then. The one thing that I do and continue to strive to do is to set boundaries and know when to bend and when not to bend. For example, I am willing to help prepare some of her meals, but have asked that she request someone else to help her with her errands. When she first moved in and was leaving her hand-washed undies in the bathroom, I carried them to her room and requested that she put them in the hamper as opposed to leaving them in the sink...sometimes it takes boldness to state where your boundaries are...and to be firm - I had to carry her undies into her bedroom a couple of times before she got the message.
Anyhow, if you haven't had any luck airing your grievances verbally, because she cries, you may have better luck with a written letter signed by you and handed to her by her son. Writing down your grievances may even be therapeutic in itself.
It sounds like she is behaving inappropriately, which could stem from a variety of reasons. Unfortunately, you cannot change her or her reasons for behaving inappropriately, but you can set boundaries with known consequences - such as: "I feel uncomfortable with you rearranging my furniture/home decor. I feel that by moving my decorations/furniture, you are not respecting my tastes. If this continues to be an issue, I think we should discuss an alternate living situation where you can have more freedom to decorate as you like."
I probably don't have to tell you this, but it sounds like your husband is avoiding the conflict by hiding in his work (pretty common for men). You can ease him out of his hiding by finding a way to destress before he gets home - yoga, hot bath, computer time - whatever helps. I bet if you spend time with him after taking time for yourself, he'll be more open to listening to you. Mothers can often come between their sons and their sons' wives - it is a sign of an unhealthy attachment...perhaps a different living situation would be best in this case.