How much do Nihon Ken cost in Japan? Well the easy answer is: Whatever the breeder decides to charge.
Generally though, most go for between $500-$1500 US. Of course there are exceptions. If you are looking for a particular type, or a pup from a particular breeding, expect to pay a premium (sometimes double the usual price). Shiba are an exception to this price range. I've heard of dogs going for well over $10,000 US. In the sane world of medium sized Nihon Ken, expect to pay around the above amount. Akita pups also tend to cost quite a bit, along the lines of Shiba prices.
So total costs you will be looking could be something like this.
Pup: 100,000 yen
Crate: 10,000 yen
Vaccination: 8,000 yen
Rabies Vaccine: 5,000 yen
Shipping: 20,000 yen - 150,000 yen
There will also most likely be a few odds and ends that come that will need to be paid for, usually another 10,000-20,000 yen.
Bear in mind that these are the prices you are looking at if you can take care of everything yourself. If you go through a 'broker', or have someone doing the translation, paperwork etc for you, you will be looking at higher prices.
I think that pretty much sums up the costs and details about exporting. I'll edit this post if I think of anything. Feel free to ask any relevant questions in the comment box.
Lastly, here are some helpful links.
Nihon Ken Hozonkai (Nippo) http://www.nihonken-hozonkai.or.jp/
Kai Ken Aigokai http://www7a.biglobe.ne.jp/~kaikenaigo/
Akita Inu Hozonkai http://www.akitainu-hozonkai.com/index.html
Hokkaido Ken Kyokai http://www.doukenkyou.com/
Animal Quarantine Services http://www.maff.go.jp/aqs/english/qanda/dogcatqaex.html