Shinkansen can get you to those places, just you may be bounded to hourly train schedule.

But for Kyoto to Osaka, there are many other choices of limited express train which will get you to destination without much of traveling time difference, and it cost by half. Just take not, JR pass can't be used for subway and certain buses in Osaka and Kyoto.

For Osaka and HImeji, same as kyoto case, I believe the traveling time difference of limited express and shinkansen is 1 hour vs 45 minutes difference.

And the flight ticket from itami airport to NRT may cost even less than shinkansen from osaka to tokyo... But if you want to have an experience of shinkansen, I would say do the math first, then you might want to buy a one-way trip to experience it all the way from osaka to tokyo