economical way to travel around Japan

Hi!
I'm planning on A 25 days trip around central japan.
this is my plan:
day 1 - arriving at Osaka airport, riding to Kyoto.
days 2-6: Kyoto, Nara, Osaka (night staying in Kyoto).
days 7-8: Koya, Himeji, Kobe.
days 9-10: Hiroshima area
days 11-12: Kanazawa area (from Hiroshima).
days 13-15: around Takayama
days 16-17: Tokyo - Nikko - Tokyo.
days 18-19: Hakone - fujigoko
days 20-25: around Tokyo
how should I plan my transportation passes, in the most economical way?

thanks
Ofer

arriving at Osaka airport, riding to Kyoto

http://www.japan-guide.com/e/e2363.html?aFROM=2033_2158
Most economical way: about 1500-2000 yen by local trains or a 1-day JR West Pass for 2000 yen

days 2-6: Kyoto, Nara, Osaka (night staying in Kyoto).

A round trip from Kyoto to Nara costs around 1300 yen:
http://www.japan-guide.com/e/e4107.html

You could use a JR West Pass or Kansai Thru Pass for your airport trip and the round trip to Nara.

JR West Pass:
http://www.japan-guide.com/e/e2361_03.html

Kansai Thru Pass:
http://www.japan-guide.com/e/e2357_005.html

A round trip to Osaka is even cheaper:
http://www.japan-guide.com/e/e2363.html?aFROM=2157_2158

days 7-8: Koya, Himeji, Kobe.

The "Koyasan Free Sabic" provides some discount for access to Koyasan. Alternatively, the Kansai Thru Pass is a good value:
http://www.japan-guide.com/e/e4904.html

Highway buses are the most economical way to travel between Osaka and Hiroshima and between Osaka and Kanazawa. There are overnight buses between Osaka and Hiroshima, but not between Osaka and Kanazawa. Overnight buses are particularly economical, since they save you a night in the hotel.

From Kanazawa, I recommend to take a bus via Shirakawago to Takayama:
http://www.japan-guide.com/bus/shirakawago.html

Takayama to Tokyo is most economical by bus. There is an overnight bus during the summer holidays only:
http://www.japan-guide.com/e/e5908.html

The side trip to Nikko is most economical by Tobu Railways:
http://www.japan-guide.com/e/e3805.html

For the side trip to Hakone and Fujigoko, I recommend the Fuji Hakone Pass:
http://www.japan-guide.com/e/e2358_014.html

For the days in Tokyo, I recommend a Suica prepaid card:
http://www.japan-guide.com/e/e2359_002.html

Thanks for the answer!
anyway, I was thinking more on public transport passes (including trains), couse I like to make my rides shorter and I don't like night buses...
can you tell me what passes should I buy, cause I have'nt decide if I should buy a JR pass, or several regional passes, or maybe combine both.
thanks
Ofer