Our itinerary end of March beginning of April
Haneda to Kyoto
Kyoto to Mijyama
Mijyama to Kyoto
Kyoto to Kanzawa
Kanzawa to Takayama
Takayama to Hakone
Hakone to Tokyo
Tokyo to Haneda
Should we get rail pass or individual tickets...will we not be able to get seats because we can not book in advance since our pass can only be activated once we are there? What is better economically?
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That said, it would be a brutally hard schedule for just 7 days - I wouldn't recommend it for a week.
You can see many previews of many places you are planning to see on:
https://www.youtube.com/user/thejapanfaq/videos
What am I better off buying? A pass or individual? Can individual tickets be purchased from Canada ahead of time?
You can see regular fares, routes and schedules on Hyperdia.
http://www.hyperdia.com
Be aware though that you'll be in Japan during Golden Week, which is a peak holiday travel season. Trains and popular places will be jammed or worse. If you know your schedule, you should make seat reservations for all your trains to get the one you want.
It is though wisteria season, which you can see and enjoy - something you'll never forget. The Ashikaga Flower Park north of Tokyo is one of the best places to see it.
https://goo.gl/EvSI3v
The shibazakura will also be out near Mt. Fuji.
http://www.japan-guide.com/e/e6919.html
Kansai area (4-5days) - including Nara
Kyoto or Osaka to Miyajima (roundtrip)
Osaka to Tokyo one-way?