I just found a document outlining a plan for my first trip to Japan. This was actually well before I knew that TheTravelDepartment.ie existed, but the plan I made actually ended up being more-or-less the same.

Japan 2006

All times are total estimates and might conflict.

5 nights:           Tokyo <-> Nikko
                      |
5 nights:  Nara <-> Kyoto <-> Osaka
                      |  Himeji (on the way)
2 nights:         Hiroshima
                      |
2 nights:           Tokyo

• Enter Narita — Daisuke/bus/train to Tokyo
• Tour Tokyo (4~ days)
• Take a daytrip to Nikko (1 day)
• Shinkasen to Kyoto (seeing Mount Fuji from the train)
• Tour Kyoto (2 or 3 days)
• Daytrip (or 2) to Nara (1 or 2 days)
• Daytrip to Osaka (1 day)
• Leave Kyoto early in the morning, some JR train to Himeji
• Tour Himeji during the day
• Leave Himeji on last Shinkansen (19:50) to Hiroshima
• Sleep in Hiroshima
• Tour Hiroshima (1 day)
• Sleep in Hiroshima
• Leave for Tokyo in the morning (4 hour Shinkansen)
• A few days to relax in Tokyo before back to Narita (2 or 3 days)

Ireland

• Book some accommodation (though Tokyo may be ok)
• Buy plane tickets (900-1000 EUR)
• Buy JR Rail Pass (310EUR)

Narita

• Get JR rail pass sorted before leaving.

Tokyo

• Daytrips
  • Nikko
• Accommodation
  • Capsule Hotels
  • Daisuke
• Touring
  • Akihabara
  • Tokyo Tower
  • Shinjuku
    • LOVE sign
  • Harajuku/Shibuya
  • Edo-Tokyo Museum
  • Studio Ghibli Museum (must investigate)

Kyoto

• Daytrips
  • Nara
    • See the Shika at Nara Kouen!
    • Daibutsuben at Toudaiji (biggest wooden building)
    • Yakushiji
    • Asuka (maybe a second daytrip)
      • Houryuuji (oldest wooden building)
  • Osaka
    • Osaka-jyou (Osaka Castle)
    • Doutonbori (Big street)
    • Tsuukonkaku (Kyoto Tower)
• Accommodation
  • Ryokan or Minshuku
• Touring
  • Aug 16th is O-Bon (with bonfire on Daimonji)
  • Kinkaku-ji
  • Ginkaku-ji
  • Kiomizudera
  • Nansen-ji
  • Ryouan-ji
  • Gion (old quarter — geishas, kabuki, etc)

Himeji

• Himeji-jyou (Himeji Castle)

Hiroshima

• Accommodation
  • No idea yet
• Touring
  • Genbaku Dome
  • Kouen around Genbaku Dome
  • Miyajima
    • Shika and Saru! (Deer, monkeys)
    • Torii (gate)

Tokyo

• Accommodation
  • No idea yet
• Touring
  • Finish anything missed the first time around.