If you need to rent a cellphone check out Global Advanced Communications http://www.globaladvancedcomm.com/. I rented an IPHONE from Global both times i visited Japan, its helpful for using Google maps etc. which will help you navigate Tokyo. The price for 2 weeks is about 9,680円.

For a longer visit I would recommend the Citadines Shinjuku & Kyoto, I got a sweet deal last summer and paid about $100.00 a night. It’s a BEAUTIFUL apart’hotel; it has a small kitchenette for light cooking and they also offer really cheap breakfast buffet that you can take advantage of. They often have winter/summer promotions so I would just keep checking their website (under promotions link).

http://www.citadines.com/

http://www.tripadvisor.com/Hotel_Review-g1066457-d1418991-Reviews-Citadines_Tokyo_Shinjuku-Shinjuku_Tokyo_Tokyo_Prefecture_Kanto.html

http://www.tripadvisor.com/Hotel_Review-g298564-d1750043-Reviews-Citadines_Kyoto_Karasuma_Gojo-Kyoto_Kyoto_Prefecture_Kinki.html

For cheap flights/packages I’ve used both Kayak and Expedia. On my first trip I was lucky enough to find a flight/hotel package on Expedia for $1500.00 for a TWO WEEK TRIP!! Just make sure to shop around and look for flights/hotels of off-peak seasons (usually around the beginning to mid Sept.)