You're right that it'd be too crowded to put all that info in the Story section, and well, the charts you have laid out for that look good already.
It probably would be a good idea to make a separate section for reference though, specifically for the chapter and episode title translations. That way, if someone starts a thread about "Ougon no Jidai" or "Danzai Hen: Bakusa no Shou", our Japanese illiterate will be able to participate too simply by looking up a reference on the FAQ.
Perhaps you can place sort of an English/Japanese Berserk Glossary as one of the sections of the FAQ. That could cover the Chapter/Episode titles, as well as list a bunch of common terms in the Berserk universe that are altered greatly between English and Japanese (rakuin/brand, shito/apostle, etc).
Thoughts?