Hi,
Yes, you have made a good plan.
You can use the Pass on the N'Ex. Within Kyoto there are a few JR buses that take the Pass, but by and large you need to take city buses and subways. There is a separate Kyoto city bus pass you can use, but when streets are crowded, traffic can move very slowly. You can use the JR Pass to get from Kyoto Stn to Arashiyama as well as the [Fushimi Inari Shrine].(https://www.youtube.com/watch?v=EandKTAwfOM "Fushimi Inari Shrine"). Fushimi is the most time consuming; you could spend a couple of hours to over half a day if you want to romp over all the trails, but the other 2 places don't take nearly as long to see. In Arashiyama don't miss the Otagi Nenbutsuji, which is one of the most humorous and whimsical places you could visit in Japan.
In Tokyo, a few of the best places to see are the Tsukiji Fish Market, plus the site that every last tourist goes to see, the Sensoji Temple. If you are in Tokyo on a Sunday afternoon, be sure to go visit Harajuku to see the youth with their wild fashions. Meiji Shrine and Yoyogi Park are next to it and well worth seeing also. And be sure not to miss the Shibuya Hachiko intersection especially on a weekend when it looks like half the city is crossing the street at once.
You still have a large chunk of time in Tokyo, and you will be there in the prime time of the autumn colours, so some day trips would be well worth it. Nikko would be an ideal choice. Kamikochi is another possibility, and Hakone is nice as well.
Best of luck.