[samurai007]

All the other places besides Kyoto are in or near Tokyo, you probably don't really need a pass for those, unless you'll be riding the subways a lot that day. Kyoto is a long way away though, and it will either be expensive or slow to get there. You might try a night train or night bus, so you can sleep on the way there and arrive in the morning, but you'll miss the scenery on the way. The bullet train will get you there and back quickly, but cost a ton of money.

You may want to just skip Kyoto and visit the temple at Nikko instead.