Unless you have a specific interest in seeing the Hiroshima museum (which is located in Peace Park, so they're not really two attractions) rather than something you need to cross off your list, I'd suggest skipping it and taking Kyoto at a more leisurely pace. (Hiroshima Castle is a reconstruction. If you want to see a reconstructed castle, the one in Osaka is only an hour southwest of Kyoto by commuter train or 20 minutes by Shinkansen, and if you want to see a genuine castle, the one in Hikone--that's Hikone, NOT Hakone--along the shores of Lake Biwa, is an hour east of Kyoto by slow train.)
Tokyo and Kyoto alone are plenty for a seven-day trip.
Large bookstores usually have maps of both Tokyo and Kyoto in their travel sections. Use these to cluster your sightseeing, so that you see the sights in one part of a city on one day, as jib71 suggested, instead of zigzagging around. For example, Tsukiji--Hama Rikyu--Boat ride up the river--Asakusa, plus the Ueno area if you're feeling ambitious, is a good itinerary for your first day.
If you haven't already, invest in a guidebook for each city.