Am I reading this correctly that you're planning to do all of this stuff as daytrips from Tokyo? I'd advise against it. For example, Hiroshima is not really within range for a day trip. It's around 400 miles away, which means probably 3-5 hours on shinkansen (never done it direct). Not to mention that the ticket will be be over $100 each way. I'd probably advise spending maybe a week in Tokyo and then going to other cities (Hiroshima, Kyoto). If nothing else, I would spend some time in Kyoto and then do day trips to Kobe, Hiroshima, Nara, from there.