Hello & salaam...
Glad to hear a muslim wants to come to Japan - especially one that loves Japanese culture!
If you pray salaat then here is a link to my local mosque, it's very nice and definately worth a visit:
Tokyo Camii & Turkish Culture Center 東京ジャーミイ・トルコ文化センター , Tokyo Mosque , 東京 ジャーミー,東京 ジャーミィ, 東京 モスク
If you get here and need any help like finding places that sell halal meat or halal restaurants (yes we do have some!) let me know!
Bye