To everybody: thank you very much for providing valuable input and a feedback. Upon its review I decided to re-sequence my travel plans and they now look as follows:

September 11: arrival to Tokyo (NRT) 15:30, transfer to Tokyo, check-in to the hotel.
September 11-14: Stay in Tokyo (Courtyard Tokyo Ginza). Some side trips by rail are possible.
September 14: Train to Kyoto
September 14-17: Stay in Kyoto (Westin Miyako Kyoto).
September 17 (AM): Train to Hiroshima, day in Hiroshima, afternoon ferry departure to Miyajima, night in Miyajima (Ryokan-type accommodation tbd).
September 18 (PM): train to Narita, check-in to one of airport hotels (Holiday Inn Tobu Narita as a possibility)
September 19: Departure from Narita 11:30

I am planning to buy 7 day railpass which would cover Tokyo-Kyoto-Hiroshma-Narita (in this case I will need separate ticket Narita-Tokyo on day 1).

Comments to itinerary above would be greatly appreciated.
AX