This is what I found. This is not my project, but a wordpress blog called "Gamer's Haven" the site's owner was making a translation patch for the game during 2009. I think his nickname is fallensaviour and he abandoned project since then (or released on a unknown platform). Here is the his project page and blog: https://fallensaviour.wordpress.com/2009/08/14/chocobos-mysterious-dungeon/
So do you know who he is? Any idea to reach him? Maybe he can at least give us the his dead translation patch and it would be much more easier to play than a full Japanese version. I really want to e-mail him.