i lived in Japan two years and have oftened travelled back for fun.
- buy the following book guides: Japan guide and the Tokyo guide (DK Publishing versions); for Kyoto - Lonely Planet version; either new on Amazon; or better yet used copies of older editions from Amazon - very cheap!. the new editions are immediately out-dated upon publication for restaurants and hotels anyways. So used copies of older editions are very good price performance
- for a multi-week stay, definitely plan for at least 3-5 days in Kyoto!!!!! it was never bombed in WWII so you see temples standing for 500-1,000 years. Kyoto is the 'ying' to Tokyo's 'yang' in Japanese history and culture. Kyoto = ATF!
- for most amazing souvenir, acquire a temple stamp book aka goshuincho - each shinto or buddhist temple or shrine will red stamp and then kanji calligraphy its name and date of visit (for a few dollars each)
- hotels & meals can be very inexpensive if you adhere to the Japanese "sarary-man" economics of super cheap domestic businessman traveling hotels and super-cheap workman's lunch spots - there are also many student hostel & eating spots
- also, if you have days, consider a 3 day hike along the Nakasendo (Kisokaido) trail through the Kiso Valley - where the samurai families beginning in 1600 began yearly mandatory visit from outlying districts to the Shogun in Tokyo.....it is worth a "splurge".....you can purchase a 'self-guided' tour package from okujapan dot com - they will provide detailed map and book you into overnight inns each night as you progress from 17th century town to the next 17th century town (amazing!) ...... it starts at an intermediate Bullet Train stop between Tokyo and Kyoto
- re Tokyo, we did 3 days with boys as follows: (Day 1) Imperial Palace, Nihonbashi Bridge - mile 0 of Japan, Yasukini war shrine, Kamiyacho government district, Omote-Sando shopping district, Harajuku pink hair district, Meiji Shrine, Shibuya shopping district, & Roppongi, then dinner at Shabuzen where Lady Gaga always visits; all connections by subway to/from Akasaka district hotel
- (Day 2) early AM to Tsukiji fish market, Hamarikyu Park, ferry boat up Sumida river to Asakusa shrine district; then subway to Shinjuku district including famous Golden Gai bar district; dinner at inexpensive Tonkatsu restaurant
- (Day 3) early AM to Ryogoku district for Sumo matches, Edo museum, Metropolitan Tokyo Museum, then to Ueno district for park and amazing National Museum & more shrines around Ueno park including one dedicated to Tokugawa Shogun .... splurged for super expensive sushi dinner at Hotel Okura (the beheaded shrimp was still wriggling!) YMMV
- re "affordable" & very nice business hotel in Tokyo & Kyoto we searched on booking.com for central locations near major subway stops....the "b" hotel chain caters to domestic business travelers, is excellent & priced well below the usual premium "gaijin" hotels if you don't like capsules or hostels, their rate included breakfast!