I have a hard time following your questions.
I've visited Japan recently, including Okunoshima. I'll give you my thoughts. We brought the Japan Rail 7-day Pass, all of our train travels were done with the pass. We did Kyoto, Hiroshima, Okunoshima, Miyajima, Fukuoka and Nagasaki then back to Osaka all on the rail pass. We got more than what we paid for the passes.
I used
http://www.hyperdia.com/ to plan my Japan travels.
If time is limited, I would skip Okunoshima. We visited Okunoshima in the morning and Miyajima in the afternoon as a day trip. The island is deserted, a bit boring for my taste. If you loved rabbits, they are everywhere waiting to be fed. Bikes are available for rent, you can go around the island on bike in about an hour. If you decided to go I can give you some pointers on how to get there.
In my opinion, Miyajima is worth at least a whole day. I wish we had spent more time there. During Cherry Blossoms it was an amazing place.
Hiroshima is good for an afternoon. We actually took a taxi from our hotel at the train station to the Memorial site, we spent in total about 2 hours in Hiroshima.
Nagasaki is a very nice city. The Atomic museum is very extensive and informative. Glover Garden, Dejima Dutch trading post and Chinatown are some of the highlights.