I understand that in places like the U.S., homeschooling is done very systematically, and that there are associations throughout the country. I don't think Japan has an equivalent to that.
But while every child residing in Japan has the right to be educated, and the child's guardian has the duty to educate that child, there is no law/rule that it needs to be done at a school. So, it's perfectly fine to educate your child at home, and the child can typically gain a graduation certificate if the principal of the child's district school permits it. (You need to talk to the principal for details.)
To get more information, you can talk to the school your child attends, in the order of homeroom teacher, grade head teacher (学年主任), sub-principal, principal, and if that doesn't work, the board of education (since it's a public school he attends). Meanwhile, you can also get information through your school counselor and your local city hall. The information they can provide would be about public organizations such as counseling services and the so-called "free school"s.
Meanwhile, there are also private-run organizations that help you educate your child. You can find them through the internet, and various paper information. For example, newspapers and bulletins (広報紙) often print ads of events that these organizations would run.
they are all at least 4 years old and may not have complete information.
You are right, but details would vary depending on your situation. Talk to the people I've mentioned. Have specific questions ready when doing so. You'd typically be talking for an hour or two per person. By that, you can narrow down your problem. Then you could come back here to ask more specific questions. But perhaps by then, you'd be finding better places to discuss it, such as local parents groups.
worry about making mistakes in the complex Japanese system.
You can't really make any big mistakes when your child is 14 yrs old or younger in Japan. But if I were you, I'd try to discuss it with as many people as possible. And the golden rule to avoid mistakes is to not do anything to fool your child. Not telling everything is fine, but it's best to accept the person as he is and to trust the direction he's heading to.
I am getting conflicting information
If you can tell us what that conflicting information specifically is, perhaps someone here can analyze it.
I do not want to do or say the wrong thing and get myself on some ' troublesome person list' here in Japan.
One thing you can do is to constantly make yourself verbally clear that you want to "cooperate" with whoever you're speaking to. For example, let's say you're talking to a teacher. By telling the teacher that you want to "work together" as parent-and-teacher, you can prevent yourself from looking like a "monster parent" who just wants to attack the other party. Again, be sure to talk to your homeroom teacher at the beginning stages. I don't really think it's a nationality thing. Every human being wants to be trusted rather than to be ignored. (Again, if the homeroom teacher is the problem, you can talk to the grade head teacher, and so on.)
My son was forced to be homeschooled, a long time ago in his early teens. For me, the key to anything I call "successful" was to talk to a lot of people, including neighbors, and to bow deeply whenever I gained help or asked for something. You don't really have to bow, but bowing is such a quick and easy way to show your sincerity and trust in Japan. As long as I bowed, I was free to say anything wrong!
I don't know what your problem is or what you want to do specifically, but even during the time my son stayed at home, I went to his school whenever they held parents' meetings. I even joined a parents' a committee. This helped a lot when my son finally decided to go back to the school after a whole year.
I hope tomorrow is a better day for you.