Can I replace the system font just for Japanese text?
The way font handling works is your android device has files in the system/fonts folder that control the font for certain aspects of the android system. One of them is the clock, the text, etc. 

In order to change these you need to rename your font file (let's say its helvetica.ttf) to android-clock.ttf to change the font of the clock. Do this for all the files in the system/font folder to change all the font on your phone.

Now, the Japanese characters... I'm not sure if the characters are handled differently than the english characters. I assume they're not, and this is why when you change the font they look strange. It's probably because the font file doesn't have the ability to change how these characters work, and is not sure how to deal with them. You may have to find a font that is compatible with both english/japanese characters.