「i think it's possible to study that alongside the language like listening to lessons about Japanese Literature and history. Or practice reading using workbooks in Japanese Literature and History. I don't think it's impossible just needs effort and motivation.」
You're right that becoming proficient in Japanese (or any other foreign language) requires effort and motivation. You may be underestimating, however, how much time will be required, even with high levels of effort and motivation.
You mention that you "know hiragana but haven't learned katakana and kanji," This means that you are several years behind Japanese students of your same age. You mention feeling confident in math and science, but those textbooks will have lots of kanji and, for science, lots of katakana vocabulary.
You said "I still have a year before i start high school," so I'm assuming you're in either the 9th or 8th grade. Also assuming that you want to go to a regular Japanese high school (as opposed to an international school in Japan), you have a lot of catching up to do in terms of language proficiency, so I would think your first focus should be on figuring out how to improve your language skills (either through study in your home country or by attending specialized language school programs in Japan).
「I have an aunt in Japan who is willing to sponsor me but since she is busy living her own life and is not knowledgeable with how things like this works she told me that if i really want to go to school in Japan i have to make an effort myself. I also cannot ask my parents for help regarding this matter since they too have no knowledge about it」
There are several issues you will need to resolve here.
First, regarding your aunt who is willing to sponsor you, is she a Japanese national/citizen, or an immigrant working in Japan? Her sponsoring you isn't as easy as just saying "My niece/nephew wants to live with me in Japan, and I want to let her/him." Your aunt will likely need to demonstrate why it would be better for you to live with her in Japan than for you to live with your parents in the Philippines, and there are often additional/stricter checks in the case of a non-citizen who wants to sponsor a relative.
Regarding your aunt being "busy living her own life" and "not knowledgeable with how things like this work," and not being able to ask your parents for help "since they too have no knowledge about it," both of those situations are going to need to change at some point if your goal is to attend high school in Japan. For starters, if your aunt is too busy living her own life to help you, it raises the question of how she's going to be responsible for your life while you're in Japan. Being your guardian for visa purposes doesn't mean she just signs a piece of paper and says "Sure, I give my niece/nephew permission to live in Japan." She will be legally responsible for your wellbeing while you're in the country, and as a minor you will be required to live with her (unless you're staying in a boarding school dormitory), and unless she can demonstrate that she'll be able/willing to provide such support in your daily life, the immigration probably won't see her as a suitable guardian for you.
In addition, no matter how much research you do on you own, at some point both your aunt and your parents will need to be involved in the process. As a minor, you are unable to enter into legally binding agreements (visa applications, school application, etc.) on your own. These are things your parents and aunt will absolutely have to be involved in, in terms of document preparation, interviews, etc. You will have to bring them into the process sooner or later, and doing so as soon as possible will probably be for the best, regardless of whether or not you are ultimately able to attend high school in Japan.
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