Itinerary and & days JR pass

Please suggest if my itinerary and 7 day JR Pass usage seems ok as its our first trip to Japan
Day 1 - 3 Tokyo
Day 4 start with JR pass Tokyo Nikko Tokyo
Day 5 Tokyo Hakone
Day 6 Hakone Nagoya
Day 7 Nagoya Takayama Nagoya
Day 8 Nagoya Kyoto
Day 9 Kyoto Nara Kyoto
Day 10 Kyoto Hiroshima Kyoto end on 7 days JR pass
Then I buy short distance single tickets
Can I use the Shinkansen trains for all above sectors.

Thanks in advance

You have a very busy itineracy planned out for yourself. A lot of time on transport, not much time overall in destinations

Day 1 - 3 Tokyo
Day 4 start with JR pass Tokyo Nikko Tokyo
Day 5 Tokyo Hakone
JR pass is only valid until Odawara (if you take JR trains, from there you need to change rail way company). There are some Hakone passes with Odakyu, depending on what you want to do in Hakone they can pay off.
Day 6 Hakone Nagoya I guess you plan to go from Hakone to Nagoya in the afternoon. That sounds okay, because then you have the day in Hakone and evening in Nagoya. If however you are planning to depart Hakone earlier I would plan to go directly to Takayama (if Takayama really needs to stay in this itinerary) and sleep in Takayama on the evening of Day 6.
Day 7 Nagoya Takayama Nagoya If you can time it in a manner to get to Kyoto in the evening, that would give you next day at least 1 full day in Kyoto. That isn't much, but at least something. Again, I would delete Takayama and Nagoya from the itinerary.
Day 8 Nagoya Kyoto
Day 9 Kyoto Nara Kyoto
Day 10 Kyoto Hiroshima Kyoto end on 7 days JR pass
you are having only very few time in Kyoto. I personally would delete Hiroshima. But if you delete Hiroshima, then JR pass will no longer pay off (assuming that you will fly back from Kansai not Tokyo). Which is okay, because buying tickets single, means you get to use Nozomi shinkansen (the fastest and most frequent ones) as well.

Enjoy planning your trip to Japan!