Superb idea for a mod.

I'm not sure how you can make indestructible buildings? I think that's hard coded, and AFAIK only the VI campaign Forest Clearing is indestructible. cegorach may know of some more.

Of the religions, these four are your most important anyway, and you can use them for your factions:

1. Hellenism
2. Di Indigetes (Roman)
3. Celtic Paganism
4. Zoroastrianism

The others...

5. Judaism
6. Heretical Cults

...can be used in the same way they they're used in vanilla MTW/VI.

For you "events" you'll need to use eras, as the events in the game are also hard coded.

@cegorach: What does one do as regards the pope in a modded game? I have always wondered about that.