Excellent advice all around. I actually made a post to this thread last night that somehow disappeared into the big bit-bucket in the sky - have no idea what happened. It looks like most of my ideas in that post have been covered by subsequent posts except one - in case you have not yet found it, please do check out the Master Thread at the head of this forum, particularly post #3 and page #2. There is quite a bit of info about "getting around" in that thread.

Also, even if you are not a "guidebook person," I suggest getting one for ideas on what to see and where things are. It makes life a lot easier. I like Frommer's, but there are many excellent choices. I your case, I suggest the more in-depth specific city guides for Tokyo and Kyoto, rather than a general "Japan" guide. If not, than at least be sure to stop at the Tourist Information Center at either KIX or Kyoto Station and pick up maps and guides for Kyoto and Tokyo.

JR