David Jones wrote: Ive yet to work out how long I can go for but cant help thinking I wouldn't mind getting out in to some of the smaller towns in the countryside. Is that something you have done much of? It sounds like you've traveled to Japan alot.
I love Japan. I first travelled there around 20 years ago (when I was living in Korea for a while) and have been going back regularly ever since. It has become cheaper and cheaper over the years to travel there, so now is an annual/biannual trek for me. Like I mentioned in a previous post - I can show you how to do 7 nights in Tokyo for less than $1000 all-in ex AUS. For that price, every bonsai enthusiast should do the pilgrimage sooner rather than later.
I once back-packed from Fukuoka to Tokyo, so I have seen my fair share of the country side and smaller towns. However, most of the small, out-of-the way places I have seen have been stumbled upon - I have the motto when I travel that I always take the path less travelled, and it has served me well. If I ever have to make a choice regarding a route to travel, I always try to take the out-of-the way path, off the tourist trail, and it is amazing what you can just seem to "find".
Given your time-frame of 7-10 days, a visit to a rural village can be done, at a squeeze for the most out-of-the-way though. This becomes a bit tighter if you visit Kyoto as well... but Kyoto is very worthwhile - absolutely beautiful. As an aside, accommodation can be quite pricey in Kyoto, especially in peaks. So I always visit Kyoto from Osaka, where accommodation and expenses are cheap - Kyoto is one Shinkensan stop from Osaka (15mins), so it is no trouble (assuming you will have a JR pass?).
I have a few of possibilities of smaller towns to visit that I would recommend, in order of least-out-of-the-way and easiest to access, to most out-of-the-way and need to "make it a mission":
1. If you visit Kyoto, take a walk up Saga-Toriimoto Preserved Street. It is a preserved part of the old Kyoto town, a historic street lined by traditional townhouses (machiya). It is very pretty, and worth a visit, but is a little bit "touristy".
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2. The Hakone day trip out of Tokyo is an absolute must, and was still the highlight for my kids when I took them to Japan. Hakone is a tourist trail ascending the mountains adjacent to Mt Fuji by cable car, then gondola, then pirate ship. At the summit of the gondola, you can get off on the top of the mountain and walk the active volcanic springs where they still mine sulphur, and cook black eggs in the hot volcanic water - a treat if you are hungry. At this point, the view across the valley is one of the best you will get of Mt Fuji - however - you
must choose a clear day for this trip, or your view of Fuji will be ruined by clouds.
I recommend you take the trip in the anticlockwise direction, in the order mentioned above. this way you can see an important addition: The usual route back to Tokyo is to scoot back to the Shinkensan at Odwarra station from Hakonemachi wharf by expressway bus. However, I have found a priceless alternate route (the road less travelled

). Stay on the boat until the second wharf - Hakone Yumoto. There you can catch the Hakone-Tenzan bus (bus 'k'). Instead of the freeway, this bus will take you back to Odwarra via the old winding mountain route, where you pass through some beautiful old mountain villages. Get off at the Tenzan Onsen (hot springs) for what I reckon are the best volcanic hot springs I have visited in Japan. They are located in a picturesque valley, and a soak in these springs will rejuvenate your weary legs (but be ready to get your gear off

). After a soak in the springs, continue you bus journey back to Odwarra, and back to Tokyo.
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3. Ohara is a rural town nestled in the mountains of northern Kyoto, about one hour from Kyoto Station, but still technically located within Kyoto's city limits. There are a few old temples and a pretty waterfall to see, but the main attraction is Sanzenin Temple which also includes a moss garden. From Kyoto Station, the fastest way to reach Ohara is to take the Karasuma Subway Line to its terminal station Kokusaikaikan Station (20 minutes, 290 yen) and then Kyoto Bus number 19 to Ohara (20 minutes, 350 yen, every 40 minutes).
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4. Miyama is a remote, rural area in the mountains 30 kilometers north of central Kyoto. The area is famous for its traditional, thatched roof (kayabuki) farmhouses. Unlike those found in many other historic towns and districts around the country, the majority of Miyama's old houses survive as residential dwellings where people still live and work. This in turn lends a very nostalgic atmosphere to the area, and gives visitors a chance to experience the traditional, authentic feel of rural Japan.
Take a local or rapid train along the JR Sagano Line (Sanin Line) from Kyoto to Hiyoshi Station (about 45 minutes, 760 yen, fully covered by the Japan Rail Pass). Most trains require a transfer at Sonobe along the way. From Hiyoshi take a Nantan Bus into Miyama (50 minutes, 610 yen one way to Kita).
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5. A very rural and traditional Japanese village is a
fairly long day-trip out of Tokyo. The Shirakawa-go and neighboring Gokayama regions line the Shogawa River Valley in the remote mountains that span from Gifu to Toyama Prefectures. Declared a UNESCO world heritage site in 1995, they are famous for their traditional gassho-zukuri farmhouses, some of which are more than 250 years old.
The fastest connection between Tokyo and Shirakawa-go is by Hokuriku Shinkansen and bus via Toyama: Take the Hokuriku Shinkansen from Tokyo to Toyama (130-170 minutes, around 12,500 yen one way) and transfer to the bus to Shirakawa-go (1.5 hours, 1700 yen one way).
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Hope this helps.