Depending on what day of the week Day 1 is, I'd consider making the Tsukiji trip at that time. That's when you're likely to be suffering the effects of jet lag, so there's a good chance you might be up at that hour. Don't forget that Tsukiji is closed every Sunday, some Wednesdays and some other days ...
http://www.tsukiji-market.or.jp/tukiji_e.htm
After visiting Tsukiji and having breakfast you might be able to go to the Hama Rikyu En and take the river boat up to Asakusa.
If you were to do that, I'd recommend staying on the East side of town for that first Tokyo stint rather than in Shinjuku as you indicated in another thread.
For Day 2 (depending on what day of the week that is) I'd suggest "Edo-Tokyo Museum, Sumo Museum, Imperial East Garden". Don't forget that museums are commonly closed on Mondays or on Tuesday if the Monday is a holiday. Check the websites of the museums to confirm.
Then Day 3 to Kyoto. Avoid Japanese guiided tours, as jpatokal said.
Then Hiroshima - but aim for less than you're attempting to fit in there.
Then back to Tokyo - and this time stay in Shinjuku - visit Harajuku, Meiji Shrine, and Shibuya.