First of all, I'd definitely age him up a bit, or lose some of the more "adult" things about him. For example, I remember reading something (actually that someone posted on the Lounge here a while ago) about how some precocious kids can read at an advanced level, but even though they know all the words and get the gist of what it's talking about, but they don't really understand the deep meaning right away in the same way that an actual teenager or adult would. Maybe he's like that and the fact that he doesn't fully process more complicated things that he reads becomes a plot point (and the fact that he likes to memorize passages could be a sign of that, like he thinks that memorization shows understanding when it really just shows that he has a good memory for things like that). Or maybe he doesn't swear, because that strikes me as something a twelve-year-old trying to be mature would do rather than a nine-year-old. Maybe you should let him have more "fun" hobbies like art or music. Maybe he has moments where he's kind of bratty or immature or unnecessarily rude. Maybe all of this thoughts, even though they're intelligent, still have a childlike whimsy and naïveté in his understanding of the world (or lack thereof, in some cases). There are a lot of possibilities to make him more childlike, or to make his personality fit his age better.
Are those the kinds of things you were thinking of? Do you want any more suggestions? Examples? (I'm trying to think of characters that balance intelligence with age well, and maybe it's because I don't read/watch a lot of things with characters who are younger than teenagers, but I actually can't think of any examples outside of my own characters' backstories...)