My first suggestion is while you are in Tokyo, stay near Shinjuku Station. There are lots of trains and busses that gives easy access to other places from Shinjuku Station.
If, for instance, you wanted to go to Kamakura, there is a pass that goes the. There is also a Hakone pass that includes a train to Shinjuku.
https://www.japan-guide.com/e/e2358_003.htmlhttps://www.japan-guide.com/e/e2358_008.htmlThere is a NEX (Narita EXpress) train two way ticket, which will take you from Narita Airport into Tokyo. You have to use the two way pass within a two week period, which works for you. The NEX goes to Tokyo Station, and will continue on from there to different stations as an endpoint. When you ask for you ticket, make sure you get the NEX going to Shinjuku Station. You my only need a one way ticket, if you plan carefully.
https://www.japan-guide.com/e/e2359_nex.htmlThere is a direct train from Shinjuku Station to Yokohama Station, and it does not cost that much. The Shonan-Shinjuku line will cost 570 Yen each way. So get a Suica IC transportation pay-pay-as-you-go card and use it.
https://www.japan-guide.com/e/e2359_003.htmlNow for Shirakawa-Go. There are no trains there, so you will need to take a bus. There are tour busses to Shirahama-Go from Takayama from the Nohi bus line. You could either activate the 7-day JR pass and go to Takayama, or you could take a Nohi bus from Shinjuku. It almost takes at least two train transfers to get to Takayama, and is about a half an hour faster than the bus, but the bus is direct. The price of the bus varies from weekdays and weekend.
https://www.nouhibus.co.jp/english/Look around the Nohi Bus website. There is a tour of Shirakawa-Go with an English speaking tour guide. There are other interesting side trip packages on that website.
If you take the bus to Takayama, then activate the JR pass now and use it to leave Takayama, and go towards Hiroshima. A limited Express train to either Nagoya or Kyoto, and then a Shinkansen towards Hiroshima. Since you are willing to make a day trip to Hiroshima, you do not need to go all the way there. I am going to suggest Kurashiki as place to stay. There are some attractions and an outlet mall there.
https://www.japan-guide.com/e/e5750.htmlhttps://www.okayama-japan.jp/en/spot/1117If the JR pass is activated on day 5, then is will be active on day 11, so getting back to Narita Airport can be done on the NEX with the JR pass. In addition, on the way back to Tokyo, you could stop at Odawara Station, and use the lower cost gFree Areah version of the Hakone Pass. Gotemba Station and the outlet mall is accessible with the Hakone Pass, but getting to the Mount Fuji Five Lakes area is not. There is a two day bus pass that can be purchased from Gotemba Station that will get you there. I have already given you the link to the Hakone Pass. Here is a link for the passport and other Fuji passes.
https://www.japan-guide.com/e/e6905.htmlCheck out the Fujisan Fujigoko Passport on that page. There are other passes listed that would also work, so you have many options to choose from. I think the three day Hakone Pass and a two day Passport might work well for you.
By the way, there IS a JR train from Shinjuku to Kawaguchiko, so if you have no interest in the Hakone Area and the Round Course, just go back to Shinjuku in Tokyo and take that Limited Express Train. The train does travel on private tracks to get to Kawaguchiko, so there will be a surcharge for the private tracks, even if you have a JR Pass.
I hope this gives you a good outline to work from.
Good Luck, in planning your vacation.
