Hi V.,
My daughter went through and is still going through the exact same thing. What I found to help was to speak to her like a little adult. If I raise my voice, she just shuts me out and things only get worse with the crying or with the mess.
Regarding school work, I have hired a teacher to teach her all summer long, as well as once a week. I found that my daughter just lacked the confidence in her knowledge and ability. Prior to working on this with my daughter, she would have poor grades in school since she never paid attention, never wrote down her homework assignments, thus never doing them. It caused a snowball effect. One on one attention outside of school with a teacher can really do wonders.
Another thing that has helped is a very strict schedule of where she puts her things after school, a set homework time, a set bedtime, etc. I can't say it has helped out much for her messy room, but it has helped tremendously with school. I find that when I get lazy with her schedule, things get out of control.
If you want to chat more about it, let me know.