On 1 April 2013, we managed to book AirAsia flight ticket KL > Tokyo (RM371.30) and Osaka > KL (RM287). Then traveled to Japan on 26 Feb 2014 - 9 Mar 2014.
Day 1 2:45pm flight depart from KL and arrive Tokyo Haneda Airport at 11pm. Then we proceed to catch the last train to Khaosan Tokyo Original Guesthouse. Day 2 Buy Tokyo Metro One-day pass and headed to Meiji Jingu (明治神宫). Then visit to Harajuku, Shibuya and Shinjuku. Day 3 Walked to Asakusa (Kaminarimon & Sensoji Temple). After brunch and shopping in Asakusa, back to hostel. Continued walking to Tokyo Skytree. Then took a train to Tokyo Tower (东京塔). Day 4 Check-out and depart to Shinjuku Station, transfer from Odakyu Station to Odawara. We purchased Hakone 2 Day Pass. We stored our bulky luggage at Hakone-Yumoto station and packed a small bag to go up Kawaguchiko from Gotemba station. 8:30pm we reached K's House Mt. Fuji. Day 5 Next morning check-out and walked to Lake Kawaguchiko. After lunch, go back to Gotemba station and passby Owakudani (箱根大涌谷). Then back to Hakone-Yumoto Station to collect luggage. Took Shinkansen bullet train from Odawara to Kyoto (3 hours). Check-in Piece Hostel Kyoto. Day 6 Buy Kyoto 1 Day bus pass to Kinkakuji (金阁寺). Then visit to Nijo Castle (二條城). Late lunch in Nishiki Market and walked around until night. Day 7 Visit Arashiyama (嵐山) by Sagano Torokko (嵯峨野観光鉄道). Follow by Tenryuji Temple (天龍寺) and Bamboo Groves. Day 8 Check-out and visit to Kiyomizudera (清水寺). Walked along Ninen-zaka, Sannen-zaka & Kiyomizu-zaka. Finally reached Gion 祇園艺妓街 (花見小路). Had dinner at Imperial Palace area. Depart to Osaka's Hotel Chuo Selene. Day 9 Go to Tennoji station to purchase Osaka 2 Day pass (2700 yen). Tried out Cruise Ship Santa Maria (帆船型游船圣玛利亚号), passby Tempozan Giant Ferris Wheels (天保山大摩天轮). After lunch continued to Osaka Castle Museum (大阪城天守阁) and Floating Garden Observatory (空中庭园展望台). Last stopped at HEP Five Ferris Wheels (HEP FIVE 摩天轮). Day 10 Go up Tsutenkaku Tower (通天阁). Tried out Tombori River Cruise at Dotonbori area. Finally dinner & shopping at Dotonbori / Shinsaibasi. Day 11 Go to Ikeda's Momofuku Ando Instant Ramen Museum (快熟面博物馆) to make our cup noodle. Back to Shinsaibashi (心斋桥) for shopping and dinner. 7pm back to hostel to collect luggage and headed to airport. 11:35pm depart from Osaka and arrived KL safely at 5:35am the next morning.
Total expenses was around RM3.7K for everything (air ticket, accomodation, food, transport, shopping). If next trip of Japan, can consider Nagoya or Hokkaido.