Absolutely it's doable - the biggest and most frequent route in Japan on most classes of inter-city trains is Tokyo to Osaka, with Kyoto as a stop on the way.
I do still recommend getting the train pass in Canada - one less thing to worry about when you get there, and I believe it's also cheaper if you get it before hand.
Sign up for a ryokan, and if you had more time, you could also stay at a monastery in Kyoto, Nara, or the surrounding areas. The monks often let foreigners stay, be part of their evening activities, and go to a service in the morning.
Don't forget to do the Philosopher's Walk in Kyoto! That time of year will be gorgeous for it.
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