Hardly any Japanese travel agents advertize in English, while non-Japanese ones do not market packages ex-Japan, for obvious reasons.

For Japan-Asia travel, I find the best deals either involve purchasing early through HIS or one of its competitors, or using up 20/30K miles from a North American FFP.

If you can find a good fare to KUL, you'll find domestic travel (both transportation and lodging) in Malaysia is extremely inexpensive. Paying less than 2 x Y39,900 while making your own arrangements shouldn't be difficult.