「since i have a late birthday, in japan i would still be in year 3 of highschool.」 Unfortunately, schools are not likely to think that way. Instead of looking at your age, the admissions department will be more focused on how many years of education you've completed. Assuming you're from a first-world English-speaking country (U.S., Canada, U.K., Australia, etc.) the kindergarten-high school standards aren't so different from Japan, so if you've already completed high school in one of those countries, odds are schools in Japan will consider you as having already completed high school, and so not eligible for admission.
「i want to be able to study in a japanese highschool after i graduate from highschool where i live to immerse myself in the culture and study...so, i was wondering if there was any complications there?」 Again, if you're hoping to enroll under the standard admission system (i.e. not in a specific program for visiting international students), then yes, this will probably be complicated. Once more assuming that you're coming from a country with more-or-less equivalent education standards to Japan, it would be like if someone who had grown up in Japan and already graduated from high school there were to move to your country and say they wanted to repeat their last year of high school in order to learn about the local culture. There might be some schools willing to accommodate that request in some form, but it's unlikely that they'd accept the person as a regular admission.
「how would i go about finding such highschools? for added information, i have a japanese passport and i have some relatives who live in japan, so visa problems and staying there would be of no problem as they could act as my legal guardian.」 While you may or may not have visa issues that will need to be cleared, there's still the matter of housing. Since you said "i have a late birthday, in japan i would still be in year 3 of highschool," I'm assuming that you would be 17 when you arrive in Japan. At that age, you would still be a legal minor, and so not allowed to rent an apartment and live by yourself.
That reduces your options to either schools that have a dormitory or schools within commuting distance of your in-Japan legal guardians who you are living with. If your plan is to live with your relatives, you might want to start by contacting the community they live in (city hall, board of education, etc.) and asking about what sort of study opportunities they may have for you.
「 i forgot to mention that i can read and write until a middle school year 3 level if that changes anything!」
That probably isn't going to help you if your goal is to attend a Japanese high school as a regular student, because it would mean that either: 1. If you're taking high school year 3 classes, you're going to be three years behind the level of language being used by the textbook/teacher/other students 2. If you're taking high school year 1 classes, you're going to be two and a half years older than all of your classmates, which is a pretty significant difference at that age.
At the risk of sounding pessimistic, it's debatable how much of a cultural experience you'd get by attending regular Japanese high school classes for the last half of year 3. Socially, that's a time when things are winding down for most high school students - they've already established their circles of friends and club activities, and they're getting ready to move on to the next stage of their lives, so it might end up feeling like you've arrived late to a party just as it's ending, leaving you with very little time to make personal connections with classmates who are already busy with a lot of preexisting relationships.
Many people have suggested going to language school in Japan instead, and, assuming your studies there go well, you could then enroll in a Japanese university, which would allow you experience student life in Japan in a potentially more meaningful and enjoyable way than a half-year, tail-end of high school experience.
Another possibility would be to look into exchange programs between universities in your home country and ones in Japan. This is the route I took after my initial hopes of studying in Japan in high school didn't work out, and I am still close friends with many of the people I met during my year of college in Tokyo.
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