Unfortunately, the Kansai Thru Pass doesn't cover JR trains, so a fast JR Shinkansen trip to Himeji or Hiroshima isn't included.
Japan-Guide is great for figuring out your transport options. Check out the Kansai One Pass, which is a tourist-only ICOCA with discounts to most popular places.
Kansai Thru Pass
Rail Passes for the Kansai Region
For groups of 2 or more without rail passes, I would advise riding taxis from Kyoto station to the eastern and northern sites. It can save time and aggravation in periods of peak Chinese crowds and cold.