Watch out for the tax implications of working for overseas clients and getting paid overseas while living in Japan. You will be considered a resident for tax purposes if you are in Japan over a year. Your income with then be subject to Japanese income tax treatment depending on where you get paid, or how much you remit to Japan.
See the income tax guide (page 5) for more info.
国税庁ホームページリニューアルのお知らせ|国税庁
Regarding your visa, if I'm not mistaken I think you might not be able to work in Japan on a student visa unless you have your school's permission. But this is a minor problem compared to the tax situation, I think.