You probably can get snag info from the Japan forum too as there are a number of threads that have discussed budget travel in Japan.

When we went to Japan in 2008, we did a quasi-open jaw itinerary flying into Tokyo and back from Osaka. [The reason I say "quasi" is because we still had to switch planes in Tokyo/Narita on the return trip.]
A JR pass was not worth it for our regional travel because of our open jaw itinerary and the days we expected to travel so we just purchased point to point tickets.
For local transportation in Tokyo, we just purchased a couple of the 2 day tourist metro day passes. It's only good for the Tokyo Metro lines. While access to the Toei lines and Yamanote line would have been handy a few times we didn't find it that much of a hindrance traveling only on the Tokyo Metro lines.