Ah eberron, one of my favorite DnD settings(I would be using fate for it instead of pathfinder/dnd.) I love the setting. Anyways here are my ideas and suggestions. Keep in mind i haven't ran this AP
book 1: Your idea of tying it into the war is good. Of course most of the ghosts are the enemies in this adventure. I would make sure you play up that, or perhaps they just wanted to be criminals. they shouldn't be too sympathetic.
Book 2: while it is true that warforged are more accepted and common. There are a few things to play with her. First is that a good number of people don't like them and hate them. They only appeared at the end of the last war. If Leipidstat or what ever is taking its place suffered a heavy assult by warforged during the war, they might have reasons to hate them.
Second only house Carrnith knows how to make warforged, and even then it is illegal for them to do so. It is not illegal for others to do so, but as only Carrnith knows how to; their results are likely to be not as good as carrnith, and could result in a frankenstien monster.
Book 3: the biggest issue in Eberron relating to werewolves is that they have been wiped out by the silver flame by the present. of course, you could have a few surviving in the woods which means people would not believe in them till they started to see them for themselves.
Book 4: I would advise against the mournland, instead their are plenty of other eldtrich monsters to use in Eberron. You have the dark six, the Daelkyr, the cult of the dragons below, and so on. Keep it in Karnath but use one of these guys instead. I myself would go with the cults of the dragon below and maybe the daelkyr as the entity they worship.
Book 5: teaming up with vampires to stop a killer, how could this be adapted... *looks to the king of Karnath that is trying to keep the next great war from happening* yea, this one is easy, either an agent of the king or Kaius himself. I would also throw out plenty of clues and red-hearings, make people question if it is the work of the blood of Vol or another nation.
Book 6: While you don't fight Tar-Baphon here, you do stop him from being released. From what it seems this should be easy to keep as it is.
From what I have read about the AP is that things are not as tied together as in other APs, for this matter I would use the order of the Emerald Claw as the big bad for the AP, with their leader being Tar-Baphon or his expy you are using.
Keep in mind they were once a respected knightly order in Karranth where they were the elite of the elite. Now though they are disgraced and tied to the Blood of Vol, and function as terrorists. It also has the effect that any Karranath Nationalists would be rather supportive of stopping them, for they are hated in Karrnath since they give a bad name to their kingdom.
I hope this gives you ideas and helps you out. :)