[Tsuwabuki]

If there's a legit reason to hang out in Japan (and five months of school should definitely do it) for a while, I don't see why immigration or customs should have an issue. As far as I am aware there is no specific law that states "you get an extension if you are waiting for a work visa." In fact, I think Japan prefers, but does not require you, to wait outside of the country.

I know that you now can no longer do a visa change. As of July 2008, you must exit the country, go to Korea, pick up your initial work entry visa, and return. It can be a matter of hours if you plan it correctly, but the ability to change your visa at the immigration office is no longer possible.