Hello,
The plan looks pretty good. Although if you are already seeing Tokyo you can mainly skip Osaka in the daytime since it's pretty much a clone. But visiting Kobe would be good, and after a day of seeing Kyoto you can still enjoy Osaka in the evening, such as at Dotonbori, and the gorgeous night views from the Umeda Sky Bldg.
For Miyajima, please note that there are 2 ferry companies there - make sure you go to the JR one if you want to use your pass. Miyajima is mostly famous for the Itsukushima Shrine with the giant "floating" torii, however the Daishoin Temple is also a must-see place. There are several other pagodas and temples, and climbing Mt. Misen offers a fantastic view over the island and whole area. If you still want more to see, then a bit past Miyajima is Iwakuni with its iconic historical bridge and mountaintop castle. And Onomichi is famous for its temple tour and wildly ornate Kosanji Temple. Nara is also an excellent recommendation - the Todaiji Great Buddha is a stunning place you will never forget. Himeji is also within reach, with Japan's finest castle.
Best of luck.