Well, I tried modifying the font by deleting the letter "E" in caps in all fonts viewable, but for some reason when I booted the game, the letter E was still showing up. :/
I'm hitting a wall here that I can't wreck. xD
That's probably because the (2?) uncompressed fonts you modified
were not what you're looking for.
Which makes sense, sort of, since they're 8x16 and the in-game font is 16x16.
Relative search with the in-game JP kana order didn't give away anything so I guess even the text is compressed in this game.
EDIT:
Well, the story text isn't directly visible for me, but at least the tutorial text is uncompressed.

This bit of text in particular is at 0x038BDD.
Table file looks something like あ=00, ア=50, 1=A0, A=AA.
Some notable control codes:
F0=<white>
F1=<red>
F6=<space>
F7=<line break>
F9FF=<end of text box with button press wait>
BTW, I find the existing English font to be ugly, so it might need to be changed (shouldn't be too hard though)