The thing about working in tech in Japan is that whereas Japanese engineers are good at making games and consumer electronics, they are not very good at typical desktop or web software. In my experience, most "software engineers" in Japan were actually Chinese... who could also speak English. Thus, it isn't that hard to get hired, even if you don't know much Japanese. It is hard to find the job in the first place, though.
There's two routes: traditional software development in big corporations where it's all Japanese university graduates or with smaller proto-startups with a bigger mix. They're not clustered in anywhere in particular. If you have contacts, give that a shot.
Living in Japan 4+ years now, I just have to say ignore recruiters unless you have a financial background. All the interesting stuff is under the radar and small companies here are desperate for creative people.
All the action is in Tokyo, Kyoto, and Nagoya.
Wherever in the world that you think of moving to, by all means, take a 2-3 week vacation there first. There is no way to know you will be happy on the ground without being there for a while to experience it.
