I'm heading to Japan at the end of September and am currently trying to work out a itinerary. There is no strict time limit as we're heading to South Korea after and haven't booked tickets yet, but we can't afford much more than 24 days.Overall it looks really nice to me.
Day 1-5 - Tokyo (including day trips to Kamakura and Nikko)Sounds good.
Day 6 - Yamanouchi (Is it worth going to Yamanouchi around this time of year? Will monkeys be bathing? How long would you suggest to spend there?)I think overnight is fine or as a day trip, most people would only spend an hour at the snow monkeys. Not sure on how good it will be when you travel, hopefully someone else can answer.
Day 7-8 - Kanazawa (How long should we stay?)
Day 9 - Takoyama (how long should we stay?)
Day 10 - Takoyama/KyotoIt is probably a little easier to go Takayama - (bus) - Shirakawago - (bus) - Kanazawa - (train) - Kyoto.
You could consider an overnight in Shirakawago in a traditional farmhouse:-
http://www.japan-guide.com/e/e5950.htmlEven if you don't stay overnight Shirakawago is worth a visit, 3-4 hours during the day is fine.
Also, if you are coming from Nagano to Takayama you can either go by train via Toyama or you could consider adding Matsumoto (for Matsumoto Castle) onto your itinerary and then take the bus from Matsumoto to Takayama which is much quicker.
Matsumoto:-
http://www.japan-guide.com/e/e6050.htmlDay 11-13 Kyoto & Nara trip.
Day 14-15 - Mount Koya
Day 15-16 - Osaka
Day 17 - Kobe (how long?)I would probably drop Kobe and reduce Osaka to one day to increase time in Kyoto, but as always it depends on your interests.
Day 18 - Miyajima (how long?)Overnight is fine if you can budget for it, alternatively it is a nice day trip from Hiroshima, just check the tide times for your exact day (link at bottom of the page):-
http://www.japan-guide.com/e/e3450.htmlDay 19 - Hiroshima (same again, how long would you reccommend?)I think one day is fine for the Peace Park, Museum and A-dome, plus whatever else you wish to see in Hiroshima. I usually recommend a visit to the Mazda Museum and Factory if you have any interest in cars/manufacturing. English tour starts at 10am and finishes around noon, it is free you just have to book.
http://www.japan-guide.com/e/e3405.htmlDay 20 - Nagasaki
Day 21-24 ??? Is there anywhere you can suggest we visit? Obviously along the same kind of route as above.If you want to stay on Kyushu, then maybe Kumamoto, Mt Aso, Beppu?
We will be getting the ferry from Kyushu so don't have to worry about a return journey to Tokyo.Not sure if a rail pass will pay off, depends how you use it and what you do at the end. It will probably at least give you flexibility and convenience. Alternatively, there might be some cheaper options with individual tickets and some bus trips.
If you do stay for 24 days and decide on a 21-day JR Pass, then don't activate it until Day 4 when you go to Nikko, so that it is still valid on Day 24.
Which pass (or not) works really depends on your final itinerary. Note that sometimes you can save a bit by condensing the main travel away from Tokyo into 14 days.
Any help would be much appreciated!Hope this helps! Enjoy your trip!