First off, Japan usually doesn't issue visas for as short as 90 days. Six months is the general minimum.

Secondly, it's now legal to obtain or change a visa from within Japan.

If you are able to and chose to come to Japan without a visa, and can't find a job in 90 days, you can either extend the 90 days for an additional 90, or fly Cebupacifc really cheap to another E. Asian nation. Then return for another 90 days. Like the extension, this can generally be done only once per calendar year.