As previously mentioned, don't activate your JR pass on the Kibune day. Also if you're just planning on using it to go from Kansai to Tokyo and back it might not be worth the cost for a 7 day pass. When i travelled from Kansai to Tokyo it was only about ~20,000 yen per trip or so (reserved and nozomi train you can't take the nozomi nor reserve with thr JR pass unless you pay the difference but why lol). So unless youre planning on going to other prefectures the pass will pay for itself otherwise do not get it.

From personal experience, Nara was only a half day trip for me so you can definitely shuffle destinations from packed places to this day.

Kibune day is quite a stretch but not impossible if you set out early.

Since you're spending a lot of time in Kyoto slap some money into your IC card and take advantage of the bus fare of only ¥200 within the city.

Don't go to Osaka too late because everything closes at like 8-9PM which is like???