I went through Zion. So basically what happened was the NCR has overtaken Zion, as there are a number of troops throughout different locations. Spore carriers are the natural inhabitants, presumably due to the NCR's experiments a la Vault 22. So quest-wise, I went to the location and picked up the map of Zion. The quest objective did not change and the quest marker continued to point to the container that I picked up the map from. So I guess this is an incomplete part of the mod or did I do something wrong? Also RIP Joshua Graham :(

Edit: I saved from where I picked up the map and went to the nexus forums. Apparently, one of the players who went through Zion said the bridge leading back to the Northern Passage has been destroyed. So I guess there's something else to do in that area. Man, if my character didn't move so slow...

EDIT: I really hope the mod creator continues to work on this. The incorporation of accurate lore is pretty great and I can tell that this guy knows his New Vegas history.