Hi Jess! Collected advice I've given friends traveling to Japan below. Have a great time :)
Get a Japan Rail Pass and a Pocket Wifi and a SIM card: https://www.japan-rail-pass.com/jr-pass
Study Japanese: https://www.wanikani.com/
Buy a hidden pocket from Eagle Creek: http://shop.eaglecreek.com/undercover-hidden-pocket/d/1130
Take at least $1000 cash, you're very unlikely to get robbed but split your money between your belongings in case you lose something. Remember to change money at the airport, very hard to find exchanges elsewhere.
Post Offices are your friend, they have foreign ATMs and many are able to change money as well. 7-11 is also very likely to have a foreign ATM.
Station food is amazing, eat it. Also eat at convenience stores. Ramen is very cheap and amazing, eat all the ramen. Yelp works fine over there and it's mostly used by foreigners so you will find relevant advice.
If you get stuck somewhere or need help just stand there for a couple seconds looking confused and people will come up to you to offer to help. Station employees are super helpful as well, but if you're off the beaten track don't hesitate to ask any random person for help. They will go out of their way to help you.
Useful phrases:
"Gaijin" - Foreigner, literally "outside person". You are a Guy-jinn, embrace it.
"Toy-reh wa doko dess ka?" - Where is the toilet? Also can just say "Toy-reh?" to anybody and they will show you.
"Eggo hanashimas ka?" - Do you speak English? Usually "Eggo" is enough.
"Eh-key wa doko dess ka?" - Where is the station? If you can find a station you can do anything, the employees are very helpful.
Many Japanese words are borrowed from English so you can often get by just saying an English word, especially simple nouns, with a Japanese accent. Examples: Bee-roo (Beer), Ice-oo Ku-ree-moo (Ice Cream), Beh-sue-boh-roo (Baseball).
Stay in hostels if you're looking to find explorer friends, great way to meet people.
Japan is a heavy drinking culture. If you end up drinking with people there are a couple of idiosyncrasies. There will likely be a shared bottle of beer or sake and small cups for everyone to drink out of, because pouring is a big part of drinking culture. You don't pour for yourself, if you want more look for an empty glass and pour theirs first - then try to fill your own. They will often stop you and insist on returning the favor.
Consider taking something to keep change in like this: https://www.amazon.com/Genuine-Leather-Change-Squeeze-92808BR/dp/B00VAZVYE0/ref=sr_1_2?ie=UTF8&qid=1488657904&sr=8-2&keywords=change+wallet+spiral
You will accrue a lot of change and you'll need it for vending machines, trains, buses. Try to keep at least 1000 yen in change with you.
Stay hydrated - it's hard to find water in Japan for some reason. In restaurants they will give you comically small fluid portions so fill a water bottle at your hotel before you head out for the day. I also recommend "Pocari Sweat" and "Aquarius", both gatorade style electrolyte sports drinks you can find in any vending machine. Drink the sweat one because drinking sweat is hilarious. Vending machines are everywhere but it will be hard for you to identify which of the bottles is actually just water so drink things at random. Some of the vending machines will have red and blue labels under the drinks, the red ones are served hot (literally heated in the machine). Coffee is often served this way.
Also if you take a taxi don't try to open the door, it opens automatically.
The email I sent to Noelle is below:
So I suggested a Ryokan in Narita but they've raised their prices, it's now 9000 yen a night: http://www.naritakanko.jp/kirinoya/content_e.html. Definitely not worth it.
I would suggest you stay here instead for $49: Keisei Ekimae
That last word "Ekimae" means "in front of the station". You should try to find hotels on Expedia that have that in the name, as anything close to a station keeps you centrally located. Apa Hotel Keisei Ekimae is walking distance to Narita-san Temple.
You can take a train or bus from the airport to Keisei Station (Eki), just ask at the information booth, they speak English very well.
After you get up and walk around the Narita-san grounds you should head into Tokyo proper. If you're hungry look for a "yakitori" restaurant on Yelp. There are good posts near Narita because they get a lot of foreigners, yakitori is basically just bits of chicken grilled on sticks but it's pretty amazing. Try the hearts :)
Getting from the airport to downtown Tokyo will cost between $10 and $25, depending on how long you have for the trip. The cheapest way is to head back to the airport on the free airport shuttle (Apa shuttle: scroll to the bottom) and then take the $10 Access Narita bus.
If you don't mind paying $25 instead you can take the Keisei Skyliner from the station in front of your hotel: Keisei Skyliner. You may have to go to a close station for a couple dollars, the station people can help you get directions.
When you get into Tokyo you're headed for Akihabara - take the Electric Town exit and you'll be very close to Forest of Owl. There are lots of fun things to do in Akihabara after, even if you just wander about and check out the electronics stalls. If you're into Nintendo or retro gaming check out Super Potato, I always visit when I'm in town.
If you happen to be in Tokyo on a Sunday you should go to Harajuku, Japanese kids dress up and wander about the streets, it's kind of amazing. You'll also want to check out Shibuya just because it's the quintessential Tokyo experience, especially fun in the evenings for drinks or karaoke. Shibuya crossing is the busiest pedestrian crossing in the world. They also have a huge Don Quijote store there, a bizarre department store chain that sells literally everything and usually has an arcade on 1 or 2 floors as well.
Finally you'll want to go to the Tsukiji Fish Market. This is the only destination that isn't directly on the Yamanote line. Yamanote is a circular train line that runs through all of the major Tokyo neighborhoods, you can ride for free with your JR Pass. You can get to Tsukiji pretty easily from Shinbashi.
Make sure you eat all of the raw fish you can find in Tsukiji, it's easily the best in the world.
When you get to Kyoto try to stay near the Kyoto station. The Kyoto station food court is amazing, I haven't eaten anything there that wasn't great. I think it's on the 8th floor. Kyoto Tower is right across the street and you can pay maybe $10 to go up top and look at temples. It's amazing at sunset.
There are 4 temples I always make sure I see in Kyoto: Kinkakuji, Ginkakuji, Ryoanji and Kiyomizudera. Try to time your temple visits so you get to Kiyomizudera about 2hrs before sunset, including bus time you will need about 2hrs per temple. The base of Kiyomizudera is surrounded by shops and restaurants at the top of a large hill. Find a kakigori place on your way up and eat some taiyaki if you can manage some gluten.
While you're in Kyotogo see the Arashiyama Bamboo Forest. If you have time for a day trip while you're there head to Himeji, it will take you about an hour to get there by train and you'll want at least 3 or 4 hours to tour the castle and walk through the gardens.
Hiroshima wasn't on your list but if you have a chance I really recommend you go to see the Peace Memorial. It's quite a way from Kyoto and Osaka so you can't daytrip it, but you could go late at night and stay near the memorial, then head to Bunny Island (Okunoshima) after the memorial to cheer yourselves up. The last ferry from the island leaves about 4 or 5pm and you could catch a train back to Osaka. If you're going to bunny island buy lots of carrots ahead of time, they have pellet food for sale at the ferry (nothing for sale on the island) but carrots are way cheaper, and the bunnies prefer them. You can ask at the Hiroshima station how to get to Okunoshima.
In Osaka make sure you go to the aquarium (Kaiyukan). The ferris wheel is right next door and connected to the mall with the petting zoo and Legoland. You could spend all day right there. I've only been to Osaka once but we only spent a day there and did exactly this. There is a great Okonomiyaki restaurant across from Legoland, Osaka is known for it. Hiroshima also has Okonomiyaki in a very different style so try it in both places if you can.
That's all I've got, you're going to have an amazing time. Make sure you eat everything you see and take lots of pictures, I want to hear all about it.
Enjoy,
Jonan
p.s. If the hotel you are booking on Expedia has the option to include breakfast take it, it's always significantly cheaper when included with your stay and universally amazing. So much better than the BS continental nonsense they do in the states. It's usually a buffet style with Japanese and Western options, it will give you a chance to sample a lot of Japanese food for cheap.