Travel advice: Get a Japan Rail Pass. The max duration is 21 days, and it lets you use any JR transportation with a few exceptions for free, this includes Shinkansen. In 21 days, you can easily go from kyuushuu to tokyo, staying at every major city along the way. Some nice cities along the way too, Nagasaki, Hiroshima, Kobe, Osaka (Kyoto and Nara close at hand), Nagoya... This is without a doubt the best way to see as much of Japan as possible.
Any first time traveler to Japan should not miss Tokyo and Kyoto, there's literally a billion things to see there. I could write a massive article on all you need to go see, but it's probably a waste of time. Just check what cities you can easily get to with the rail pass, then look up on wikitravels etc what is famous in those places and you'll find a ton of shit worth seeing.
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Forgive the spelling errors, mistakes ect, and incompleteness of this post. Just throwing this together quick because I don't have a ton of time, but I know I have really appreciated all and any of the help I've received in the past from others in the TL community in my travels/endeavors. Here are some random insights and pics, hope something can be helpful.
I spent 3 months traveling in Japan, from Hokkaido to Kyushu, back in 2011, and just recently returned again from a trip a few months ago this year. If you are spending 2 months in Kyushu, I would recommend pm'ing TL user thopal. I believe he lives or works somewhere around Nagasaki, and came to hang out with me while I was in Fukuoka. Real stand up guy, and likes to meet people from TL. You can try to pm Mani if you like, as daphreak pointed out, he lives in Osaka. He's also a great person and has given me some great advice in the past. However, he's a really busy dude with a family, so just keep that in mind.
Since you will be there for 3 months, definitely get the rail pass. If you decide to travel far or often, it will definitely pay for itself.
As far as things to enjoy, that's really up to you, how adventurous you feel, and what you want to do.
Some places I enjoyed/recommend/advise/been too:
Tokyo: Ueno: Probably the most chill part of Tokyo. Has a nice park, and some parts of it have a more traditional feel to it as well compared to other parts of tokyo. The nightlife there is not so exciting, but there's a great pub next to the park named the Warrior Celt. It's a gaijin bar owned by really awesome British guy named Andy. Lot's a foreign customers and natives alike, and a really good place to gain some insight or mingle with some natives.
Few pics~ From the park
At the Celt
Shinjuku/Shibya/Ginza: Just for the metropolitan allure. lot's of ritzy stores, big malls ect. If you travel through Tokyo, there's a good chance you'll wind up at Shinjuku station anyways. nightlife is also not exciting here, and I would personally recommend avoiding the golden gai. it's basically a weird little system of alleys and small hut's masquerading as bars, and 99% of them to don't cater to gaijins and have a ludicrous cover charge.
Ropongi: Go here if you want to get harassed by Kenyans soliciting hostess bars and prostitutes and such. Pretty much a complete red light district at night. Gas Panic is a fun little club though, met a wide variety of people there. keep an eye on your drinks.
Osaka: My favorite place in Osaka so far is namba, just for the river and the arcades. Easy to get lost here, so many shops and usually very crowded, but lots to see and do if you got time to be lost. Avoid Shin Osaka, it's basically full of government buildings and a few bars and restaurants. Also, since you seem to do stuff with food, you might want to investigate some places for good native food there. Everyone always jokes to me Osaka people eat strange food, so I am sure someone more adventurous than me could find some interesting foodstuffs there.
Few Pics
Nanmba
The river~
Messin around
Kyoto: I really enjoyed kyoto. If you go to the traditional side, you'll get what you came for, however, it's generally completely full of tourists, which can make the experience a little less enjoyable. The river here is really peaceful, lot's of friendly stray cats :p. There is also a really great view of the city from Kyoto station, just take the escalators alllll the way to the top.
Some random pics~
Hokkaido: Lot's of parks and space if you are the outdoorsy type. Sapporo in my opinion was the most western looking/feeling of all the big cities I've been to in Japan. I had lot's of fun here, but I only came because I had good friends who lived there. Also, if for whatever reason you decide to go, keep this in mind. if you don't have a rail pass, i'm pretty sure you can take a domestic flight there from haneda in tokyo and get there in about 2 hour's compared to taking the bullet train that goes underwater. (I've done both). Just depends if you go straight there from tokyo or not though, if your around shin amouri or something i'd sure that'd shave off quite a bit of time.
I've been to quite a few other places, but that's all I have time to throw out there at the moment.
once peice of advice I'll give you is to go and grab a lonely planet phrasebook. It will come in handy, as it has pretty much every basic thing you need for communication, and even a reversible dictionary. If you don't speak Japanese already, you won't understand the colloquialisms and even if you get a grasp on the grammar, it could be hard to communicate. This thing will basically give you some good phrases for every situation, along with a Japanese written translation if you can't pronounce them correctly. When I first came, I was able to communicate with a lot of people I met, where otherwise I would have been lost for words or by myself all together. The bigger guidebook to japan is also very recommended, as it will have pretty much all the information you are looking for.
Also, if you are in a big city, always keep 5000 to 10000 yen on you, in case you really need a taxi because the trains aren't running (12am to 5 am) or you are lost. Taxi's are expensive, and, getting lost far away from your hostel/hotel is not fun.
Anyways, your trip can be anything you want it to be. just do some research yourself, and inquire a bit into whatever personally interests you the most. Feel free to PM me if you have any questions, just keep in mind, I am by no means an expert or an expat. Hope you have a nice trip!
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