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Japan itinerary-Help needed

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We are planning a trip to Japan for either this coming spring or fall. We are first time travellers to japan and would like to see and experience as much as possible in this trip. We have no time limit, but I think around 2.5-3 weeks in Japan would be ideal. From my reading, I would want to concentrate on scenery and architecture, and spend a minimal number of days in Tokyo. We would probably fly into and out of Tokyo as the flights into or out of Osaka are much longer from the east coast of the US.

I was thinking3 nights in Tokyo, 2 nights in Nikko, , 2 nights in Takayama, 2 nights in Kanazawa, at least 5 nights in Kyoto, apossibly yvisiting Hiroshima and or Nara as a day trip from Kyoto.

Questions:
!- Is it most cost effective to get a JR Railpass for this itinerary, or shoud we use regional passes. If JR, how many days..7 or 14?
2-In what order should we do this considering the rail connections to each.?
3- Any difference in rainy weather in either early April or Oct? i checked weatherbase, and it looks like Japan gets lots of rain in both months.
4-We want to stay at hotels which are located near train stations. We do not care if the rooms are small as long as the location is convenient to public transportation. Any recommendations for $100-$200 hotels in the above cities.
5-Any other tips for planning this trip? Would you add any other" must see" places. Again, we have no time limit, just a stamina limit of probably 3 weeks on the ground..
Thanks in advance for your help.
Shelley

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