Alrighty, deep breath, because this might be quite a bit of information I'll be putting in here.
Studying abroad over in Japan for the entirety of your post-secondary academic career is an interesting prospect in and of itself. While definitely a far more viable possibility for native English speakers nowadays compared to a few decades, you're right in noticing that it's not necessarily a straightforward process. That's the nature of study abroad in and of itself, what with the chance to pursue overseas education however you want to, but it's even more so since you want to spend a prolonged period over there instead of a typical semester or year-long setup. That said, it's definitely very worthwhile to do. I think it goes without saying that any extended period of time abroad really opens up your horizons and understanding of the world, so I applaud your effort.
But enough fluff from the introduction. Let's get down to the nitty gritty.
Assuming I'm right in presuming that you're a native English speaker with little to no education in the Japanese language, the first thing you want to do is specifically search for schools within Japan that both have a large international student population and are well-regarded universities in general. While conventional Japanese universities can at times offer some courses in English, the reality is that if you're wanting to pick up a solid post-secondary education, places like Tokyo University aren't going to be your best bet simply because of sheer language barrier issues. Naturally, you'll be pursuing language skills anyway, but it's one thing to be able to do it in a classroom and then apply it in just daily life, yet quite another to learn it in a classroom at the same time you're having other courses taught in that very language. It gets to be complex too quickly for those who are unprepared. Japanese is a great language to know, but taking in too much all at once also won't work to your benefit. Thus, the reason why I recommend checking out schools with a large international student populace is because those schools will more likely than not have their courses taught predominantly in English. As long as you verify beforehand that they're both accredited and carry a good academic recommendation, it shouldn't matter that you weren't taught in Japanese.
Three schools I thusly recommend checking out are
Akita International Univeristy,
Sophia University, and
Temple University. Akita International University is located in a mountain area with a population of around 100,000. It may not be as busy as Tokyo, but I personally recommend the area if you want to get to know a side of Japan you won't necessarily find in the popular media. Sophia University and Temple University are both located in Tokyo. Out of all three schools that I've suggested Sophia University would probably be the one that looks best on your transcript if you're concerned about that. While only their liberal arts department is English, I don't think the quality of the school itself can be overstated, as it's one of the top private schools in the country. (It should be noted that it is a Jesuit Catholic school, just so that information is out there.) Perhaps part of this praise comes from the fact that I'll actually be attending this school for the summer in preparation for another study abroad gig over in Japan, but it's still a school that definitely shouldn't be overlooked either way. As for Temple University, it's actually the only school within Japan where you can actually still get a US degree, thanks to its unique legal position and affiliation with the main university of the same name in the States. The degree types seem to be modest, but if you didn't want any potential hassle with employers seeing an international degree on the resume, then you may want to consider that school. (I doubt that it's seriously a problem with Japanese degrees, though.)
Okay. One point down. Onto the next one.
Finances. You should do some extremely serious budgeting before you head over there and I have several reasons for this. First, the cost of living in Japan can be more expensive than it is in the States. If you're careful and look around for good deals on most everything, you should do okay, but when considering that the current global economy can make exchange rates with the dollar fluctuate for better or for worse, a lot of caution needs to be exercised. Secondly, financial aid can become a tricky matter for students from abroad. I bring this up because realistically speaking, you probably won't be able to enroll in a US school and go to Japan for all four years and expect to have graduation go smoothly credits-wise. Its possible, but I would think most schools by now have policies in place which force you to do at least one semester on their actual campus, if not more. Otherwise, they can't probably consider you to be one of their students legally. If you want to do all four years in Japan, you're probably just going to need to apply to one of their schools directly instead of by proxy via a study abroad program. (Hence the reason that you don't see me suggesting US schools besides Temple University.) Tying all this back into financial aid, there are going to be more hurdles for you if you need any such assistance since, as with the US, those budgets are naturally designed with native citizens in mind first and foremost. There's still aid that you can seek out, but do some serious research on how you'll pay for it all, because it will majorly haunt you if you don't do so.
On a similar note, also look into visas. For your purposes, you're absolutely going to need to look into getting something other than a tourist visa for the duration of your stay over there. (The default one for visitors is only 90 days. It's definitely not enough.) That said, be careful with which sort of visa that you decide on, as it can have serious legal implications on what you can and can't do while you're living there. A regular student visa, for example, won't allow you to even get a part-time job legally, which may be necessary to support yourself. Do some extremely major research on this so you go into Japan at the legal capacity you need to be at. That said, you'll also need to look into how to renew whichever visa you get, as I believe it's a yearly thing for those without residency. You'll additionally need to make sure your passport doesn't expire during the time you believe you'll be staying there, if you don't have one already.
A few more things and then I think I'm done for now.
For living arrangements, I'd seriously consider living with a family if I were you. Dorms don't have the most opportunities in the way of socialization and fluency potential whereas living with a family lets you put your Japanese to very good use at any level. It may sound daunting, but Japanese people tend to be very accomodating of those who aren't especially fluent in their language. (It's not even necessarily surprising that they'll be flattered when you use even the simplest grammar points with them, either.) The great thing about living with a family is that you're forced to make things work in order to get along with everyone else, so things will probably turn out fine if you choose to go that route. I should say, however, that it's not wise to try using English; the educational system over there tends to not do an especially stellar job in that respect. You're likely to encounter more Engrish than what would be practical for your living situation.
There's a lot more that I could discuss, but I guess the last thing I'll discuss is (ironically) how you should start it all. Really, applying for schooling over in Japan is much like it is in the States; researching the schools, figuring out their admissions requirements, and then taking it from there. As I've already implicitly mentioned earlier, you should also start budgeting for it right now. Until you're over there yourself, it's wise to save up more than enough money you need so that you can live with at least a bit of breathing room until you figure things out. Also, if you can, it doesn't hurt to take a Japanese course of some sort, even at a community college. Any knowledge of the language before you go is better than none, really. I personally endorse classes over most any other method simply because good teachers can accomodate your learning style a lot better than printed text or software. If you can't do that, then I won't stop you from trying Rosetta Stone, although that's not the path I would recommend if you have any options beyond that.
If you have any further questions, you're free to PM me about it, since I've been in the trenches before and can speak the language. Best of luck to you, man!
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