I'm just going to post a little bit here to say that I am having some simialr issues with my DD, also in middle school, who is undiagnosed but kind of ASD/ADHDish. I had some lightbulbs going off because like your son, she is having more trouble in classes with less structure and organization (she has like a 105% in math right now--that teacher has a very defined system!) We are also having issues with not turning things in because there is not a defined time or place for turning in. I think in elementary this was always announced and there was a place where it always went.