If memory serves AFT files were used in Jump Ultimate stars but it could well be in other games so I do not want to call it- if you want specific help you will have to say what game it is so one of us can pull it apart and point you in the right direction.
Anyhow for something more general you likely have two problems
1) Pointers (jump ultimate stars certainly had those and although they were not the easiest to work with they did nothing drastically different). In short pointers are numbers that well point at the end or start of words (hopefully not but it can happen), sentences (more common), paragraphs (not as common as sentences but common enough) and larger sections that the game reads and jumps the "cursor" to rather than scanning to text and figuring it out (a costly process and one weaker embedded devices can ill afford to waste resources doing). I usually like to make an analogy between the contents page of a book and pointers as they serve to perfom roughly the same task.
2) Text box limits. Even with the best will in the world on the part of the pointers you will probably still get a nice example of Japanese being a compact language when compared to European languages. You might get lucky and the game has a scripting engine or sorts that will allow for extra boxes to easily be added but otherwise you will be upping limits or changing what the game wants to load at various stages. This is usually quite doable though.
If you were on the GBA or dealing with text found in the binaries (can and does happen) you might have issues of how to cram it into the file but as long as you steer clear of making your translation thirty times larger than the original you should be OK if you are just editing files (one of the nice things about working with the DS and other systems that use files rather than bundle it all together). Equally not all parts of a game use pointers as they might use something to parse through or they might have sections of a fixed length but those are usually reserved for special cases (simple games in the case of the former and menus,bestiaries, in game encyclopaedias and such n the case of the latter). I should also say pointers are not always simple numbers from the start of the file and can be offset by an amount (add say 20h to the pointer and you get where it is at in the file- the 20h will usually be the length of the header or something) or be relative (where the pointer is then add the pointer value to that- if the pointer is at 34h and reads 46h you go to 7Ch).
As for the characters you have two main options
1) The game might well use shiftJIS meaning you have some Roman characters there as part of that ( http://www.rikai.com/library/kanjitables/kanji_codes.sjis.shtml )
2) Hack the game to support ASCII either by overwriting part of the Japanese font with Roman characters or actually hacking the game to use 8 bit characters (enough for just about every European language character) which is what the patch for Jump Ultimate stars eventually did although the former requires you to fiddle with a tile editor (easy enough if you have ever used paint or something like it) where the latter will see you learning some assembly for the DS. The bonus of the latter method is you usually gain more than enough space to make up for lengthier nature of European languages.
