HI there!
Yes - you can use the Bullet train from Tokyo to Kyoto (using the Hikari shinkansen). You can also use the JR Pass to get from Narita to Tokyo via the Narita Express or normal JR trains.
The ticket office in Narita Airport is open from 6:30-21:45. It also fills in for the time when the JR Pass Exchange office is closed (which is perhaps where you have the strange times from):
Narita Airport Terminal 1 Exchange Office hours
JR EAST Travel Service Center: 8:15-19:00
Ticket Office: 6:30-8:15, 19:00-21:45
Narita Airport Terminal 2 Exchange Office hours
JR EAST Travel Service Center: 9:30-20:00
Ticket Office: 6:30-9:30, 20:00-21:45
You can purchase tickets from the ticket office at any time between 6:30 and 21:45 of course :)
Hope this helps!