I'll have 6 weeks to explore Japan between August 20th-October 3rd.Sounds nice.
August:
20-22: Tokyo (is PASMO the best way to travel in the city?)Pasmo or Suica, yes.
http://www.japan-guide.com/e/e2359_002.html23-24: Nikko (3,600 yen round trip for 2 days)
25: one more day and night in Tokyo
26: a long journy to Sapporo. activating the Hokkaido & East JR pass for 7 days.As mentioned above, might be easier/cheaper to go from Nikko.
27-31: traveling around Hokkaido.Where? I usually recommend Hakodate, morning markets are good fun and the mountain would be nice in good weather
http://www.japan-guide.com/e/e5350.htmlSeptember:
1: journy back to... where? I need to get somewhere in 24 hours.I think it will be difficult to head west. I would probably just go back to Tokyo.
Question: will the seishun 18 cover the busses between Kanazawa, Shirakawago, Takayama and Kamikochi?No, Seishun is for trains.
Is there a good deal to travel between those places?The only real option is by bus, not covered by Willer Express. Pricing is detailed on each of the individual city pages on japan-guide.
What is the recommended time to spend in each of them?Depends on interest. I think one day in Shirakawago is fine, you could consider an overnight stay in a Gassho Zukuri. Takayama 2-3 days, Kanazawa 2-3 days.
I'm still trying to decide whether to include Toyama and Nagoya in my itinerary. Do you want to see anything there?
If I do, how shall I do it from Takayama area?By train would be best, bus is possible too.
I can take a buss from either Toyama or Kanazawa to my next stop - Kyoto.Ok.
Arriving to Kyoto around 5-7th of September?
Activating the 5-days Kintetsu Rail Pass and traveling as so:
-two days in Nara
-one day in Ise
-two days in Nagoya?
-back to KyotoSeems fine.
11-18: exploring Kyoto
19: Night-buss to Hiroshima. Exploring the city.
20: Miyajima. (If I'll change the order of things and be in Hiroshima before September 10th, I can use the seishun 18 for the Miyajima ferry. Worth considering?)The ferry is only 170 yen each way, so I probably wouldn't try and re-arrange just for that.
21: Hiroshima to Fukuoka. How long should I spend there?2-3 days I guess. Depends on what you want to see.
I can take a buss from Fukuoka to Osaka, but I guess two weeks in Osaka is too much. Any other suggestions?
My interests are mostly nature, old architecture, nightlife, and if there are any festivals I don't know about...Two weeks is probably too long in Osaka. Maybe consider visiting parts of Shikoku? Maybe include Tsumago and Magome before/after Kamikochi? Matsumoto after/before Kamikochi?
Tsumago
http://www.japan-guide.com/e/e6077.htmlMagome
http://www.japan-guide.com/e/e6076.htmlMatsumoto
http://www.japan-guide.com/e/e6050.htmlYou can probably loop these by doing something like:-
Nagoya - Tsumago - Magome - Matsumoto - Kamikochi - Takayama - Shirakawago - Kanazawa - Kyoto
If you went Tokyo - Nagoya at the start, this might mean you don't need to use two days of the Kintetsu pass to go back to Nagoya from Kyoto.