I have some problems with japanese input in LFS.
First, I have the same problem as you had, Scawen with the question marks instead of kana and kanji. You solved it by setting japanese as the default for non-unicode applications. Is this the only way to do it? Being French, if I do this, kanji appear instead of characters like à é è etc. in other applications and some fonts become strange.
The second problem is this:
This message appears each time I select an alternative conversion for kana/kanji (with spacebar). I do not think it is related to the question marks, because it also happens when I type romaji (latin characters).