Honeybadger, your son's scores bear a lot of similarity to my D's. She is 16 now, but had MANY of the same characteristics at his age. She has grown out of some, others not so much. She was diagnosed with a non-verbal learning disability (it was mentioned as a possibility when she was in 2nd grade, but we didn't really pin it down until 9th grade). She, too, had a lot of issues with facial recognition.
She still struggles with executive function issues. Just this week she ended up with points off on 3 pre-calc homework assignments because she didn't get them turned in on time. They were done on time, just not with her when she went to class. Then she forgot to deal with it for a couple of days. She also has trouble remembering to put her name on assignments. I think she does her homework twice more often than she admits because she can't find it after it is done. She carries a 3.7 GPA (unweighted, but she does take all the honors classes offered at her high school) -- it would probably be a 3.9 (no hope in French even if she were organized

) if she didn't have the executive function problems.
She also has always had trouble putting her thoughts together on paper. She has fabulous analysis skills (I, too, could see a PhD in literature or philosophy in her future!), and in a verbal class discussion those qualities really come out. But it is hard for her to get it out on paper. She is fine at grammar, spelling, and vocabulary. Just not great at considering her audience and putting together a logical flow in a paper. In fact, we are trying to get her school to allow her to take an online AP Lit & Composition for the rest of this year instead of their normal English class partly because it would be very writing intensive, and that is what she needs the most this year.
In fourth grade, she also was not a sparkling conversationalist at dinner, and not always even intellectually curious when I would expect her to be. She has certainly become more so on both over the years, especially more intellectually curious. She was kind of internally focused for a lot of years, I think. Also, she is NOT a people pleaser (my older kid is, but she is not). So grades are only marginally important to her, and she wants to spend time on her own stuff (reading, biology, studying for Quiz Bowl, Doctor Who

). She does what is needed, but usually not more.
Things that have helped us over the years:
- A high school with block scheduling (so they only juggle 3 or so academic classes per quarter) has been good for D.
- She has gone to an independent, private school with pretty small class sizes. A lot of the teachers are relatively forgiving on organization issues, especially because she has a diagnosed disability.
- Daily paperwork sorting/organizing sessions with both of us involved. We don't do it daily any more, but we did pretty much all the way through ninth grade. Sorry, I am sure you don't want to hear that. But she just couldn't do it. She has gotten somewhat better -- not more organized in keeping things in folders and stuff, but she is more likely to know where she stuffed the paper when she is looking for it later. She asked for a new set of school folders for Xmas (Santa is all over that!).
- She has a laptop (everyone in their high school school does, and they carry it pretty much everywhere). She has started using the calendar function more effectively this year. Sometimes she uses a sort of sticky note function to put a reminder on her computer desktop for things she has to do.
- She has contact with friends from school via email and chat on her computer, and can confirm questions about assignments and due dates with them when necessary. Since she doesn't always write down the info when she should, that is her backup process. I suspect she does this a lot more than I even know about.
- Her slow processing speed in math has improved somewhat over the years. She does have accomodations in math class to have extra time on math tests, and the teacher puts one problem per page on her tests. She has also been granted time and a half from the College Board on SAT/AP tests due to her non-verbal learning disability (because of slow processing speed in math). She is actually very good at math (is considering a career in epidemiology, which requires pretty good math skills), just a little slow.
It is frustrating, but to some extent we have to take our kids as they are. I try to feed her areas of interest, and work with her to shore up her skills to an acceptable level in her areas of weakness. I was a really frustrated parent (especially in middle school) until I accepted that she has a learning disability that affects her executive functioning. Once I accepted that she needs extra support in that area, and we were only going to take babysteps (and sometimes slide backwards), our relationship is better. I'd rather have the solid, loving relationship we have today than a higher GPA with more friction in our relationship.