I'm trying to help people like yourself come to Japan. Feel free to contact me: http://www.tokyodev.com/jobs/

If you have a university degree, it is actually pretty easy to get a visa here. While you might have trouble getting a job at a 3-person startup, something a bit more established shouldn't be an issue (as the article mentions, Gengo recruits non-Japanese, and they'll even hire people who aren't already in Japan).

The easiest way to get a job here is the same as anywhere else: be exceptional at something that is in demand.