Ya...I think you should just buy the tickets separately.
7-day rail pass is 28,300, which is about two Shinkansen tickets for Tokyo - Kyoto/Osaka (You don't really need Shikansen for Kyoto-Osaka).
Buying them separately...you can take Nozomi...which is faster (less stops) and runs more frequently.
Also JR is not so useful in Osaka...not to mention Kyoto...