Tokyo to Kyoto

Hello, we will be traveling from Narita to Tokyo where we will be staying 5 days, then leaving for Kyoto. We will be in Kyoto for 4 nights, then back to Tokyo for 2 nights, visiting Disneyland. I am not sure if the JR Pass will work for us. If we activate the pass for the Narita Express when we arrive, we will probably not need it for the 5 days in Tokyo, other than maybe a side trip or two. That leaves us with one day for our trip to Kyoto before it expires. We would have to pay for the return trip to Tokyo, and the travel back to Narita for the trip home.

Is there any option for us that might be best? Thank you for any help.