If you haven't booked a place to stay, I would recommend the Budget Inn in Kyoto. They have a "golden room" that's really nice. And Toyoko Inns are a hotel chain that has a lot of locations, and English sites.
Also, the JR rail pass, the kyoto bus pass (500 yen/ day) are good deals.
If you're heading to Kyoto, you might also want to try Osaka and Nara, which are only about half an hour away.
Obviously, Akihabara in Tokyo for electronics and anime. There are the small stores and Yodobashi and BIC (larger stores). Yodabashi also has several blocks in Shinjuku. There's also an area in Osaka (not too far from Kyoto if you have time) that is also famous for electronics (my friend swears by it), near Dontonbori
I would warn about letting your daughter wander around though, some anime sections are not children appropriate.
A good anime store is called Animate, there are locations all over...I just visited one in the shopping area across the river from Gion in Kyoto
My must sees are Asakusa at night (bring a tripod), karaoke if you've never been, sumo (there's a tournament in March in Osaka I think), Meiji shrine near Harajuku, the Edo Museum in Tokyo, Kiyomizu in Kyoto, Fushimi Inari shrine (kyoto), Bamboo forest in arashiyama (kyoto), Kinkakuji and Ginkakuji Osaka Aquarium, Daibutsu and deers (nara), Gion (kyoto) at night
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