Erica

• If you know someone there, get them to help you with a lot of stuff ahead of time. You'll need a Hanko to sign your apartment lease, apply for a bank account, etc. and having that the moment you arrive saved me a ton of headaches, as did having a lease ready w/ keys to pick up once everything was signed for.
• You'll need a valid japanese phone number for a lot of stuff, like a bank account, and those are hard to get if you're not a permanent resident. I was able to get a phone number from a low-tier carrier that had a booth at Bic Camera. Unless this has changed, au/docomo/etc will not sell you a non-tourist data plan because of anti-trafficking laws.
• The Japanese post office is also a bank. They were the ones who were the kindest to me (a foreigner) wanting to open a bank and there's post offices everywhere, so I highly recommend them.
• I had to figure a lot of this out myself because I kept working freelance there and planned for a much longer stay. I did not want to rent a temporary apartment through an agency or anything so I can't help with that. If you get a job ahead of time that'll figure out the paperwork for you then that's great. If not, again, plan to have someone who speaks the language there with you because you'll need to register your address at the Ward Office, both to be registered as a citizen and to register for healthcare.
• Nitori is a chain of furniture store that are like Ikea except their stuff is nicer and they do free delivery/installation.
• Get ready to use Facebook because a critical resource are expat FB groups that sell stuff if you need it/need to get rid of it, or can offer you advice when you're there if you have no one to ask.

That's all I can think of off the top of my head!