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Don't do hotels. Look for "executive apartments" or short term residences. You won't get anything like hotel, but you can get a decent place for a month at about the same rate as a decent hotel for a week. Most of the facilities are located reasonably close to public transit, which is very important.
It is easier to stay in the bigger cities, it gets harder the further outside of the major cities that you go because of the language issue. In most of the major cities, at least some of the signs for transit and stuff have english translations. Go outside of the biggest cities, and everything turns solidly japanese with no translations and often very few people that can understand you.
Taking a japanese language class or self teaching at least the basics of communication would help.
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