I have some suggestions: First, find a male mentor, someone other than yourself or the homeroom teacher -- such as an older student or teacher -- who meets with your son at his school a few times per week about staying on track for projects, cleaning out the backpack, and generally following through on some goal completion. I have actually done this in high schools, where the elder student volunteered his or her time as a service project. Our kids get tired of hearing our voices and often another young person, a positive mentor, has a better chance at being heard.
Second, I like the book, Why Bright Kids Get Poor Grades by Dr. Sylvia Rimm. It has many helpful suggestions for encouraging academic independence. I don't really think of giftedness as an excuse for distracted behavior. I have told gifted teens that while it's okay to be lost in thought periodically, not to forget Pierre Curie: a brilliant scientist who was also lost in thought over his research, when he stepped off a curb and got run over. What a waste! Gifted students can learn to put some personal responsibility first.