[Teris]

We found a hotel near Tokyo Station. Here is our slightly revised itinerary. Please let me know what you think! Thanks everyone.

Day 1: Arrive Narita. Activate JR pass and take Narita Express, hotel shuttle or limousine bus to Tokyo Station. Stay in Hotel Ryumeikan Tokyo near Tokyo Station.
Day 2: JR pass to Kyoto in morning, check into Super Hotel Kyoto Shijo Kawaramachi. Walk around Kyoto.
Day 3: Kyoto
Day 4: JR pass day trip to Hiroshima (stopping at Himeji despite construction).
Day 5: Kyoto, check into Ryokan Shimizu.
Day 6: JR pass to Tokyo, check into Hotel Sunroute Plaza Shinjuku. Spend day in Tokyo.
Day 7: Nikko (last day of JR pass)
Day 8: Tokyo
Day 9: Tokyo
Day 10: Hang around Tokyo, take Narita Express (or bus) to Narita, fly home in evening.