I didn't need any shots when I went. Not sure how long getting your first passport takes though, since I got mine ages ago. As for advice:
Bring a little plastic bag for rubbish when you go out. There are very few trash cans in public; mostly just recycling bins by vending machines.
Study up on manners. They're very big on this. Don't do stuff like talk on your phone on trains or eat while walking.
A lot of stuff is in English so it shouldn't be too hard to find your way around, but being able to read Hiragana and Katakana is very helpful just so you can understand Romaji.
Rent a wireless router. These little things are so incredibly helpful :3
They sell adult magazines in 7-11. Riiiight next to stuff like Shonen Jump. I just wanted to bring that up.
One more thing: Japanese dubbed movies are hilarious. Seeing Will Smith "speak" Japanese in MIB literally made me laugh out loud.