Tokyo -> Kyoto -> Hiroshima -> Osaka -> Tokyo

We have planned following travel plan.

Tokyo -> Kyoto -> Hiroshima -> Osaka -> Tokyo

Is there way to confirm all the trains on above routers are covered by the JR pass.

Are there any trains that are not covered by the JR train pass. Seems like JR pass also allows one to use Hop-on-Hop-off buses in selected cities, is there a list of such cities. Also are there specific companies with which you can use the JR pass?

Also the web site indicates that if I select green pass, I need to select the seats before boarding the train, is that correct? Do we get to select those seats just before boarding?

-Subodh