I haven't read any of the other posts so I don't know if my opinion is simmilar or way different.
Many kids in Jr High WANT to be independent, or their parents want them to, but they just aren't ready. Especially the boys.
You have two choices:
The first, let him fly on his own, get the bad grades. But keep in mind this may not faze him. Or he may give up, seeing no results. Or it may just close doors to him early on (eg by not doing well in a math class, his poor work habits may keep him on a lower track unnecesarrily, he may not be eligible for more advanced classes).
Choice 2, continue to monitor- constantly . if he is getting his organizer signed and checked daily by a teacher, at least you know what is due every day and what to make him study for. then make him do it. At the end of every night, go through to make sure it is all done, put it all in the appropriate folders so he knows where to find it when it is time to turn it in, and tell him how proud you are of what a thorough job he did that night (even if it was mostly you helping organize it). I understand you still have no control over whether he turns it in at the point... but let's think about baby steps here... if he can't be responsible for that one little thing on his own (taking it out when the teacher asks for it) then he REALLY isn't ready to be responsible for the whole she-bang, start to finish, with no help from you.
Personally, I would stick with the monitoring. Some kids just need that more than others to get it done. I am a school counselor for Jr. High and I actually feel really bad for the kids who are so bright and capable, but organizationally or motivationally challenged, that get not support from their parents because the parents think they should be doing it all on their own all the sudden. That's what parents are for- to guide, supervise, lay down the law, build up the habits.
I think I don't have to say this but obviously I am not talking about actually doing the work for the kid, just sitting them down and making them get through it. And making it your business to know every little thing they have to do for the next day.