September 22 days itinerary

hi!
We have a general draft of an itinerary, and I'd like to have your opinion on how to order the itinerary best:
1. Tokyo (including 1 day in Fuji Q park) - 6 days
2. Nikko - 3 days
3. Alps (Kamikochi, Kiso Valley, what else should we do?) - 3 days
4. Hiroshima (including Miajima, and Shimanami Kaido) - 3 days
5. Kyoto + Nara - 3 days
6. Osaka - 2 days

some questions:
1. what would be a good order, in order to minimize difficult travels, and minimize costs (a.k.a - utilizing a JR pass probably)
2. I read it is possible to buy to-and-return bus tickets including entrance to Fuji Q park for about 7500Yen PP, but couldn't find how.. is it really possible?
3. How should I handle the Shimanami Kaido? I wish to do it in one day, where should I start and where should I finish - in terms of transportation to the next destination

Kyoto and Osaka are within 30 minutes of each other. So I'd just combine the two.

The order you have listed your travels is okay in sequence of travels.

I'm with @Hakata14 regarding Osaka, Kyoto & Nara They are ideally placed to stay in one location & visit the other sites. Osaka to Kyoto is 30 minutes & 560 Yen by train and a ticket to Nara is about 800 Yen. I personally would take a day from Nikko & add it to the Osaka/Kyoto portion of the trip as there is so much you can do there.

Regarding the Shimanami Kaido. If the weather is nice it's a lovely day out. The easiest way given your itinerary would be from Onimichi to Imabara. There are three buses a day back to Onomichi, see this old thread, Unfortunately the linked homepage is only in Japanese & mainly images so wont go through Google Translate. https://www.japan-guide.com/forum/quereadisplay.html?0+134927