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Japan in September - Itinerary & travel recommendations please!

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We will be in Japan for 16 nights in September (1st-16th) and I'm trying to finalise our itinerary and am looking for comments on thoughts to date. I know September is typhoon season but it's the only time we could go :-/
We have spent a week in Tokyo before (2005) and so are not planning on spending more than a day there on this trip (on top of starting/ending there). We really want to do some hiking and so I'm trying to build in 5/6 days in the mountains.
Having ploughed through many existing threads and got many ideas/helpful links, my focus is on managing the first phase of the holiday which is the hiking bit.

The best hiking seems to be in the Kamikochi area, and I fancied doing the Alpine pass. But now I'm thinking that for that first week perhaps we should hire a car to see the mountain area, returning to Tokyo to then catch a train direct to Kyoto. This would give us greater flexibility and avoid scenarios of carrying our luggage on & off buses - which is the only way to get to Kamikochi. Not sure if dropping off the car somewhere other than Tokyo would be too expensive - or whether that expense would be worth the convenience.

So latest thoughts (now changing by the hour!)

1. Arrive Tokyo
2. Sightseeing Tokyo
3. Drive to Kawaguchiko
4. Day of walking, admiring Mt Fuji (too late to consider climbing it!)
5. Drive to Matsumoto, see the castle etc, drive on to Kamikochi
6. Hiking
7. Hiking
8. Drive on to ... ? Somewhere in the mountains, like Kiso-Fukishima
9. Drive back to Tokyo, train to Kyoto in the evening. Or drive to Nagoya, leave car there, train to Kyoto?
10. Sight seeing Kyoto
11. Sightseeing Kyoto
12. Overnight trip to Koya-san
13. Back to Kyoto, sightseeing
14. Train to Hiroshima, sightseeing Hiroshima
15. Day trip to Miyajima
16. Hiroshima to Tokyo
17. Fly home

In my train/bus instead of car version the variations I've toyed with are leaving out Kawaguchiko and head straight for Kamikochi but overnighting in Matsumoto to break the journey and see the castle there, and also whether to do the Alpine route or not. I really fancy doing it but the logistics - with luggage - may be challenging, and then the question has been whether to overnight in Toyama or Tateyama and then head straight to Kyoto, or go on to Kanazawa and then Kyoto (ie one less day in Kyoto, spent instead in Kanazawa).

We are people who enjoy travelling and usually plan full-on trips that take in as much as possible. But I realise that this isn't, say, Switzerland: it's a very foreign land where the trains may also run on time but I won't understand a word that comes out of the PA system, or where to get off a bus! Which is why after reading other posts I'm now thinking about the first week in the car. My partner loves driving, and we tend to do at least one road trip holiday a year.

Many thanks for any thoughts on the itinerary and if anyone has ideas for good hiking locations that fit in with the broad direction of travel I would very much appreciate them.

Angie

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