Yes, unfortunately... you need to create layers in AE (basically, I don't have the mood to make a separate AE interface - it will be easier for me if I use pre-existent interface)...
Well it's basically like this...
Select the text layers you created (with text styles and lead-ins/lead-outs effects and in-syllable effects) varied by the names (Kanji 1, Romaji 2, etc)
(You can also select image layers or video layers [for other overlaying effects], etc)
Run the script
then you'll get hundreds of layers (you can UNDO and ram preview if you want to)
Render it
(You don't need to save this product, only save your version before it gets generated)
I just started writing the script, and it will be based on objects (KRK object) because it's easier to organize.
though, it might save some ram issues if you don't display all the layers, but I'll give that a consideration if this is good to go.
The problem now is that SDK only runs on XP, not Windows Server 2003 (I only have that installed), which I find it stupid. I haven't gone through the documentation, but I'm not sure if I can use that to make use of .aep, or it's only for the plugins.
And, thanks for the suggestion
Edit: another thing that comes into mind, I can make a script such that you don't even need to deal with javascript at all. You just need to template your layers and effects, and it will do the rest.