Was just there in April - tons of good advice in this thread.
Only a few nuggets I can offer:
1) Find and eat Garlic Ramen - sooooooo delicious
2) Sounds crazy, but eat the PASTA - yes, I am talking Spaghetti, etc. Best pasta you will ever eat.
3) Hiroshima is definitely worth it, and can be done on a day trip (leaving Kyoto), but most people recommend staying overnight. It is very depressing as well, so be prepared for that.
4) Rent a pocket WiFi - it is cheap, and then you have internet everywhere you go.
Other than that, Japan is one of the few places I have been to where I have NEVER felt unsafe - even on dark streets in the middle of the night. I love it there, and already want to go back.
Have fun!
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