Japan is a wonderful place to visit.
I have put this map together to share some of my favourite ways to spend my days there.
Book your flight and have a wonderful time.
Tanoshinde kudasai!
Anna

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Kagoshima : 31.132901, 130.803223
Tokyo: 35.664035, 139.698212
Takachiho Gorge: 32.711690, 131.307787
Nagoya: 35.181446, 136.906398
Koya san: 34.216667, 135.583333
Takayama: 36.146124, 137.252173
Kyoto: 35.011636, 135.768029
Hiroshima: 34.385203, 132.455293
Wakkanai: 45.415664, 141.673082
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Kagoshima
3 days to a week in Kagoshima
Hire a car, take it on the Sakurajima ferry. Soak up the awesome views of the volcano and then drive all the way down the Osumi peninsula to the southern part of Minami Osumi, near Sata misaki.
Stay in the Sata deilando ( yes, "Saturday land") cottages for a night.
Spend a day enjoying Sata and Sata Misaki Peak then the next day get up early and take the Negime ferry to Yamagawa.
Drive from Yamagawa to Kaimon dake, and be blown away by this beautiful "Satsuma Fuji".
It's quite a and hike, but definitely do-able with a bit of effort and well worth it for the breath-taking views at the top.
Stay here to recover and have a hot-sand bath:
Hakasuikan Ryokan
The dinner is just delicious. I loved it so much they let me have one of the Kagoshima maps they use as part of the place setting ( a simple Japanese paper "washi" sheet they lay over the starters before you arrive). I've even framed it.
Spend the next day driving up to Chiran, make time to reflect at the Second World War museum and the samurai village before driving back to Kagoshima city.
If you have any longer, then go up to Kirishima too... More amazing hikes,
volcanos, lakes and onsens.

Kagoshima Prefecture, Japan
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Tokyo
I'll have to add to this over time. But here is a starter...

Begin at the Omotesando -Aoyama dori crossing. Soak it up a little, grab a coffee and stroll down Omotedando towards Meiji dori. Look all around you as you walk along, as there are some amazing buildings along the way. I don't particularly recommend actually going in the shops along the main road here -they are just all the top end luxury brands... - but do explore along the side roads and pop into little shops and boutiques there if you want to be tempted.
If you keep going ( only about a kilometre) then you'll come to
Meiji shrine. It will take an hour or so to walk up and around it. Chances are you may even see a wedding taking place there too.
Spend some time mooching in Yoyogi park if you're in the need of greenery. It's a magical place to people-watch on a Sunday as there are loads of musicians, actors and dancers practicing routines, as well as families, couples and kiddies just getting out for some air.... With some of the most unique dogs you'll ever see.
Otherwise, re- track your steps and head back down Omotesando, past Meiji dori to " Cat Street" on the right.
It's a funky, pedestrianised road to pootle along which takes you to Shibuya.
Bright, brash, bustling Shibuya ...
Make your way to Tokyu Hands department store...if you want, well almost anything. Everyone loves it.

Go for a run around the Imperial palace
Have a ( very expensive) coffee at the top of the Mandarin Oriental and see the view of Fuji. Or just go at night and look at the views.   Or have similar views at the top of the Ritz in Midtown.
Have brunch on the Two Rooms terrace.

Have dinner at Andys and he'll tell you all you need to know about visiting tsukiji fish market, and may even take you there if you ask nicely.

There is so much more to do in Tokyo...  but you'll have to go and explore for yourself!

Shibuya, Tokyo, Japan
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Takachiho Gorge
Takachiho gorge
You can even hire a boat and row down it

Takachiho, Miyazaki Prefecture, Japan
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Nagoya
Nagoya:
I really enjoyed living in Nagoya. I think it deserves more attention than it gets as its a perfect size city to cycle around and is also perfectly situated for trips out from there. I was based there in 2005 for the Aichi Expo.
If you're into pottery, check out these little villages nearby: Seto and Tokoname.

 

Nagoya, Aichi Prefecture, Japan
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Koya san
Koya san. A very special place in Wakayama.

Go here for peace, greenery quietness and general time out. You can stay in temples if you book early, and are prepared to get up very early!

Koya-san, Koya, Wakayama Prefecture, Japan
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Takayama
Takayama, a trip back in time... similar to a mini-Kyoto.
With delicious food ( as always) at the end of each day

Takayama, Gifu Prefecture, Japan
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Kyoto
Kyoto:
You need several days to see all the highlights, but Kyoto isn't a place to rush. May be you just have to go back more than once.
You must see Kinkakuji and Ginkakuji of course, oh, and Kiyomizudera and walk around Gion at night. Go up to the top of the Kyoto Station building too. You'll need to refuel at some stage, so try and schedule that while strolling along the Philosophers walk, and just before you get to the Heian Shrine.
Take a day or a afternoon in each of these places:
Fushimi inari
Arashiyama

Kyoto, Kyoto Prefecture, Japan
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Hiroshima
Hiroshima
My favourite thing is Hiroshima is the Mazda factory. Can your believe you can go in and actually watch the most amazing car in the world, a MX5, being built?
Of course, you must also visit the:
Peace museum
Miyajima
and eat okonomiyaki

Hiroshima, Hiroshima Prefecture, Japan
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Wakkanai
Wakkannai 
If you're going to go to the southern tip, you may as well go up north too, right?

Food is delicious, loads of signs are even in Russian, and you can go out for boat trips to nearby islands.

Wakkanai, Hokkaido Prefecture, Japan