Why are you doing two day trips to Hiroshima? Do Osaka as a day trip from Kyoto and then move to Hiroshima for two nights. The trip back to Tokyo/Narita on the last day isn't hard (or too long IMO).
And, the train routes are pretty simple (I do them all the time). I would suggest Tokyo-Toyama-Takayama-Nagoya-Kyoto as that covers the complete trip through the mountains and across the main island. I normally spend two nights in Takayama so that I can take guests across to Shirakawa-go (or you could check the Hida Mura (folk village) as well as more of the town.