What time is your return flight?

We just got back from Japan. Our final night was in Kyoto. We caught the Shinkansen at 0956 and reached Narita around 1330.
If your flight departs after 1700, you could spend 5 nights in Tokyo and 2 nights in Kyoto. However, that will give you only a day and a half in Kyoto-You'll need more time than that.

Jay71 has a good suggestion. Leave Kyoto for a future visit.