Looks like you found Sakura, which is good. For real estate - the further from central Tokyo/big cities, the cheaper and more reasonable. For that reason, anything outside of the the Yamanote line will be a start. If outside Tokyo Met, then Chiba is a good prefecture, as is Saitama (Saitama is up and coming). Kanagawa is more expensive than either of these areas.
I'd start by seeing where you can find employment first, then live nearby accordingly.
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