I use Android in English but also need full Japanese support, to read and type. To achieve that, I replace Android's ( rather poor ) DroidSansJapanese.ttf with IPAPGothic
and doing so I get a good proper font. Easy, just renaming IPAPGothic as DroidSansJapanese.ttf and putting it in :
Then to avoid Android using the font DroidSansFallback.ttf, I replace as you mention the following file defining fonts with my own :
I don't touch anything else and it works for me on 4.1 and 4.1.1. Android uses IPAPGothic for Japanese in my devices and DroidSansFallback.ttf for other languages needing glyphs. I also replace DroidSansFallback.ttf with a better font that supports full Traditional Chinese and Korean, by the way.
Here's the fallback_fonts.xml file I use in case you want to check it or use it directly. ( If so, rename .txt to .xml and also remember to make sure permissions for the files you put in system/ are rw-r--r--
Hope it helps.
Edit : this is a bit of a hack to preserve naming from Android 2.2 and 2.3 ( DroidSansJapanese.ttf as it is called in those versions ) and don't erase the MTLmr3m.ttf font in Android 4 in case I need it for anything or Google changes something later on, but again, it works for me, so maybe worth a try.