I'm not really sure whether anyone could help here because considering the massive amount of mods out there, I don't think it's very likely that a low profile NPC mod would have been tried and completed by many people.

I've got past the Underdark after getting Jeralias soul from the Demon in chapter 2 I've killed Amaralis and saved Kiara after been abducted by Bodhi, now there's two possible paths here. Either kill the prelate as the Demonlord asks, or disobey his instructions by doing something else, which I currently have no idea what it is at the moment, but I read in FWS that you were supposed to help Jeralia and that would have an effect on things, but still I can't find anything, is there something else I am supposed to do before going to Bodhi? because if so I'm screwed. Any help or advice is appreciated.

Not having played the mod, I can't directly answer your question, but I would suggest posting it here: http://forums.forgottenwars.net/index.php?showforum=89

It's the official forum for the mod, and it is monitored quite frequently by those involved in the mod's production. They'll be able to give you a quick answer. :)