I'm assuming you will be using Japan Rail Passes for the long distance travel. In that case, I'd suggest activating the Passes to start on Sunday and getting the combined Narita Express/subway card for the trip in from NRT and subways around Tokyo. That way, the JR Pass covers your train travel throughout the rest of the trip AND the Narita Express on your departure day.

The days look fine. Most hotels will not allow you to check in before 3:00 pm but if you get to Kyoto earlier, you could certainly drop off luggage and come back after 3 to actually check in. The hotel will hold your bags.

As for travel times, the Hikari shinkansen takes about 2-3/4 hours for Tokyo-Kyoto. I'd advise avoiding the prime business travel times early and late in the day. Frankly, I think I'd take that extra half-day in Tokyo, check out of the hotel at 11:00 am and catch the noon train to Kyoto. Pick up a bento or other lunch and eat on the train, arrive at the hotel about 3:00 pm, check in and then go out to explore some before dinner. Some of the best of Kyoto is best seen at and around dusk - Gion, Pontocho, etc.

Thursday, I'd wait until after 8:00 am to go to Himeji - you don't want to get there before they open the gates at the castle. Plan on having lunch in Himeji and returning to Kyoto - or going on to Kurashiki after lunch. If you go to Okayama or Kurashiki after Himeji, you will not get back to Kyoto until after dinner time. Otherwise, use the afternoon to see whatever you missed in Kyoto during the first couple of days.

For the return to Tokyo, I'd do it in the morning, drop off my luggage and see some more of Tokyo that afternoon.

JMHO. JR