Although you may be aware of their presence, Chabad does have a center in Tokyo. Even if you are not pursuing a chabad lifestyle or orthodox conversion, they are a very good resource, a good place to start and may even have classes or whatnot - a link to Judaism while so far away. Their contact info is below. You also mentioned you have lots of questions about 'aspects' - could you be more specific?
Address:2-27-23 Ebisu
Tokyo, Shibuya-KU 150-0013 JapanPhone:81-3-5789-2846Fax:81-3-5789-2847Web:
www.chabadjapan.comRabbi Mendi SudakevichMrs. Chana Sudakevich
Best of luck!
Naomi