Hi guys, any tips comments will be appreciated.

I will be flying out Monday, arriving Haneda Tuesday 10:25pm
check in hotel
Wednesday - explore Tokyo
Thursday - explore Tokyo
Friday - train to Kyoto, explore Kyoto
Saturday - Hiroshima, Miyajima (important question here, should these places be avoided on Saturday?)
Sunday - Nara and whatever else (will anything be closed on Sunday? will I have problems taking the train back to Kyoto?)
Monday - hang out in Kyoto and spending the night at a Ryokan
Tuesday - take train back to Tokyo
Wednesday - Hakone day trip I think
Thursday - tbd if I can do another day trip with 7 day JR pass
Friday - Tokyo or whatever
Saturday - Tokyo or whatever
Sunday - check in out

thank you all in advance

also I read Tsukiji is closed on Wednesday is that true?