Make sure that you get the rail pass while in Canada. It cannot be purchased once you arrive in Japan. Also, if you're trying to save money you might want to get the one week pass and just plan it so that you leave Tokyo and arrive back once the pass expires. Otherwise, buy the two week pass because you can use it on the above ground rail system in Tokyo (you still have to pay for the subway because it's a different transit system).
I would suggest backpacking. I didn't have much trouble getting around and was able to leave my bags at the hostel most of the time. I found that, the comfort level between the hostels and the low-to-mid-level hotel was mostly the same.
So much more that I'd like to talk about. I spent 3 weeks there by myself and saw almost all of Honshu (the big island), but I travel pretty hard. Beyond Tokyo, definitely you should plan to see Kyoto and the nearby town of Nara, which is where Japan biggest temple is. Kyoto was my favourite city because you get a taste of urban life, but there are hundreds of beautiful temples on the outskirts of the city that rest serenely on the sides of mountains.
I'd also plan on going to Hiroshima. Beyond the Peace Memorial Museum (about the atom bomb), there's also a great temple at Miyajima (a little island in Hiroshima's suburbs) that is fantastic. One of the most beautiful spots I've encountered.
In the Lonely Planet guides there are a couple of itineraries that give you a good idea of what you can hit in 2 weeks.
I know there are some CPers here that can give you great ideas. Enjoy yourself. I was really jealous when I saw that discounted price in the Travel Junkie thread.
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