Most of the characters specifically being complained about there aren't even main characters in that game.  The main cast is pretty much fine, I thought. 

Little correction: seems like agemo's debugger cannot log XA accesses to the CD (Mode 2 Form 2), but only regular ones (Mode 2 Form 1). So I guess that method doesn't work and all those sectors logged are only the portraits loading.

If everything is in one single archive, re-arranging them probably wont do you much good. It'll just be a matter of time before you bump into something where one language's clip is significantly longer than the other language's equivalent... and solving that problem would either require you to speed up the audio (Uurk... I've seen some unofficial dubs of games do this) or you'd have to figure out how the index (start/stop markers) works for the audio database. The moment you've solved the latter, editing the audio would be pointless anyway, as you could most likely just take your time to convert the JP start/stop markers to whatever wonky format/layout they'd have to comply with in the EN version. Anyway, this is far from my field, but what I would recommend is probably trying to do some extensive comparing of the JP and EN version of the game and filter out everything that is the same in both versions and then start to identify the leftovers.


Anyway, not being a big supporter of undubs myself, I have to say that there might be "other" issues with dropping an audio DB from one language into another. as there's always a possibility that script editing or translation changes makes things horribly incompatible at times (additional or less lines of dialog, resulting in only partial audio playback and stuff ... not to mention potential audio/text inconsistencies created during the localization process)