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In my other life as a college professor, I used to advise students who wanted to study in Japan.
It all depends on what your ultimate goal is. Kansai Gaidai has exchange programs with what seems like half the colleges in the English-speaking world, so if you want to go to school with a bunch of other gaijin and concentrate on content courses taught in English, this would be okay. On the whole, though, it's mostly for undergraduates who want to do a junior year abroad. Same with Waseda if you enter the International Division, although not if you enter the regular programs, which is much harder, since Waseda is one of those schools that Japanese students bust their heads trying to get into. Another possibility is International Christian University in Mitaka (west of Tokyo), which isn't so Christian that you'd actually notice and is a completely bilingual university. Everyone in the regular curriculum (as opposed to jr. yr. abroad) has to master both Jpn and Eng well enough to take classes in them.
The Monbusho scholarships are for people who want to earn a degree from a Japanese university, not for short-term study.
In either case (unless they've changed the system since I left academia ten years ago), you start out with several months of intensive language training at a central location. (It used to be a school in Osaka.) After that, you are assigned to a university that is strong in your field, and you are given up to two years to study for the grad school entrance exams as a "kenkyuusei." If you pass, they will support you through the M.A. level. (Ph.D's are rare in Japan and usually go to people who have been teaching or researching for a while.)
If you apply to a university on your own dime ("shihi" as opposed to "kokuhi" i.e. Monbusho), you still have to find a way to pass the entrance exam.
I studied in Japan on a form of "shihi," subsidized by my Stateside grad school, which had just received a huge grant for Asian studies. However, since I had no intention of earning an M.A. (I already had the equivalent), I simply entered as a "kenkyuusei," which meant that I could do anything I wanted and didn't have to pass any entrance exams. My U.S. advisor arranged for me to study at a unversity where a friend of his was foreign students' advisor.
PM me if you have any further questions.
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