What pass should we get beside JR pass

Hi, we're going to Japan on end Nov, have purchased 7 days JR pass and planned to activate on the first day. Below is our itinerary

Day 1 arrive at Narita, then by shinkansen to Kyoto.
Day 2 Kyoto to Osaka visit USJ and maybe Dotonburi in the evening
Day 3 Kyoto - Fushimi Inari, Kiyomizudera and Higashiyama
Day 4 Kyoto - Arashiyama and manga museum
Day 5 Kyoto to Nara back Kyoto (pick up luggage) to Tokyo
Day 6 Tokyo - Hakone (stay overnight)
Day 7 Hakone - Tokyo
Questions:
1. Can I use JR pass in Osaka and Kyoto? If not, what pass should I use?
2. Any suggestions on my itinerary?

We will be staying at Hamamasucho area in Tokyo
Day 8 Ghibili museum , Akihabara, Shinjuku? Enough time?
Day 9 Tsukiji Market, Asakusa, Senkakuji temple...any other suggestions?
Day 10 Need suggestions here.. thinking to go Nikko, but think is too far.
Day 11 Flying home (planning to buy skyliner to Narita) what do you think?
Questions: What kind of pass should I use base on my itinerary? Is the 72 hrs metro pass better or IC card? If is IC card,which one should I get?

Thank you in advance.

IC card - which one doesn't matter.
If you go to Nikko, get the 3-day Tokyo wide pass as the JR return is around 12,000 yen and the pass is only 10,000yen and it pays off in one day, or look at the Tobu railway pass options.
Your 7-day pass will not really save you much (Tokyo-Kyoto return is less, especially with other available discount tickets), but you have it now so make the most of it.

Day 3 i think you can do your day trip to Nara with Fushimi since it is on the way so Day 5 you can just do Kiyomizudera and Higashiyama and straight back Tokyo instead.

Hakone you might wanna put in outside your 7 days JR Pass period and get a 2 day Hakone free pass instead since the cable car, ropeway, sightseeing boat isn't covered under JR Pass.

Day 9 u can slot in Akihabara in between Tsukiji & Asakusa if there isn't enough time on Day 8.

Day 10 i would suggest Kamakura instead, Enoshima is beautiful.

Day 3 i think you can do your day trip to Nara with Fushimi since it is on the way so Day 5 you can just do Kiyomizudera and Higashiyama and straight back Tokyo instead.
Only if they get the slow local train - the express does not stop at Fushimi-Inari station.
Plus, Nara has more than enough to fill a day, and Fushimi-Inari can take 1-3 hours depending on how much you explore.

Day 5 Kyoto to Nara back Kyoto (pick up luggage) to Tokyo
Day 6 Tokyo - Hakone (stay overnight)
Day 7 Hakone - Tokyo
I wonder why you would go to Tokyo on Day 5, when you can go directly to Hakone through Odawara. Not all, but some shinkansen stop in Odawara and from there you can take a local train to Hakone. That way you can stay two nights in Hakone, enjoy the onsen and do less hotel changing.

Day 8 Ghibili museum , Akihabara, Shinjuku? Enough time?
Just to warn you that you need to buy the Ghibli tickets WELL in advance. I think on JTB they open pre-sales around 3 months prior to the date of the visit. Check it out, but you will want to buy those tickets immediately. They sell out really fast (read: within hours).

Enjoy your trip to Japan!