The Asia-Pacific Journal (Japan Focus) has just published an excellent preliminary guide to approaching fieldwork in Japan, by Prof. Levi McLaughlin (Philosophy and Religious Studies, North Carolina State). In it, he touches upon

• the importance of building personal connections with professors, graduate students, librarians, and archivists at the institution where you’re based in Japan
• how to secure a letter of affiliation from a Japanese institution to begin with (for fellowship applications, etc.)
• how to approach forging contacts in other institutions or other circles, including but not limited to the groups you may be looking to research
• some tips on preparing for and conducting interviews
• documents and equipment to prepare to have with you
• managing and safeguarding your data (have backups upon backups!)
• some tips on research ethics
• among other points and topics

You can read the full article here: https://apjjf.org/-Levi-McLaughlin/3388/article.html.