Welcome to Flyertalk.

You're listing a lot of off-the-beaten-path type places, so I'm unable to answer your specific questions. But it sounds like your Jpn trip also includes other places like Kurashiki, Kobe and Osaka, so I'm wondering where else you're going and how long you're spending in those other places.

You're going to an awful lot of museums (to each his/her own, though) and allocating >2 full days in Hiroshima. Personally I've never spent more than a day in Hiroshima. I think I may have spent anywhere from 1-2.5hrs at the Peace Park / atomic bomb museum there. And it's hard to imagine spending more than like 4hrs around there, but that's just me. The city of Hiroshima itself is not much different than any other typical large Jpn city except the trolleys are pretty cool. On the other hand, Kurashiki has a distinct feel in the old section, Osaka just has everything and unmatched vibrance, and Kobe is laid out beautifully betwn the sea and the hills. Hiroshima Castle is impressive just like most major Jpn castles, but it takes a back seat to many other castles imo including Himeji which I presume you'll visit. If you're thinking about taking cranes and everything, obviously you have a passion for the place and its history, so I don't want to talk you out of spending that much time in Hiroshima. Just giving you my perspective.

Miyajima can be enjoyed in 5-6hrs, including trip up to Mt.Misen (I'd recommend ropeway up, hike down thru Momijidani). However, I think one could just as well spend an entire day there and even more thoroughly appreciate it.

I keep hearing Onomichi is really cool, so I'm glad you have that on your itinerary.