I have found that using MTools text extraction nearly never results in any breakages. I then just run it through some scripts and batch it to sugoi. Once done MTool reinjects it back into the game.
Instructions:
Load a game via Mtool then navigate to the translation tab. Click export offline...
You dont have to change system locale for extracting. In winrar (and probably others) you just open the archive in winrar, click options and then set encoding to japanese. Then extract and none of those jumbled letters occur.