Definitely order your rail card before going. Not sure if you can get the same discount by showing your passport at the station.
My aunt told me the proper way to visit Japan is to get the rail pass, take it to the end, and plot out cities to visit&spend the night on your way back to Tokyo. I was told my method of 7 days in Tokyo and 3 days in Kyoto was just wrong. I thought it worked out well.
Kyoto, while interesting, was mostly a bunch of old temples. It's an amazing location for my Japanese friends, but as a non-Japanese foreigner, the magic of the place was mostly lost on me. That said, the bamboo grove and the temple surrounded by arch-covered paths were pretty cool. (there's a sequence in Memoirs of a Geisha where Zhang Zhi Yi's character runs out 1 into the other, but they're actually a couple miles apart)
Tokyo had more things for us. Walking around Asakusa, the old imperial palace, akihabara, and the craziness of harajuku were probably my favorite activities. However, the biggest WTF moment was going upstairs at the starbucks just outside Shibuya train station and looking down at the sea of people crossing the street. I'm sure you've seen video of that before.
I wish we could have gone to Tsukiji, but the others I was with were too low on funds for breakfast there by the end of the trip. Favorite meal was Okonomiyaki&Monja.
