IIWY, I'd skip Meiji Shrine. For easier (or cheaper) access from Narita and to Tsukiji and Kyoto, I'd go for a hotel at Tokyo Station or in the Ginza/Shiodome area rather than the Keio Plaza. For Kyoto, Kiyomizudera takes some walking uphill. Taxis can't take you all the way. You might consider asking Mr. Doi to plan a tour for you with minimal walking.