A 7 day JR pass would cover you for:
(1) The journey from NRT to Tokyo (via JR N'EX then Yamanote line to Ueno)
(2) The journey from Tokyo to Kyoto
(3) The journey from Kyoto to Tokyo
(4) The journey from Tokyo to Kyoto
(5) Any other little trips you make on JR lines (but not subway rides)
Cost is about the same as a return ticket from Tokyo to Kyoto.
You indicate that you already have a ticket from Tokyo to Kyoto. If I were you, I'd consider getting that refunded (usually possible for a small admin fee) and getting a JR Pass.