Has this been discussed
-Who was the dead body in the lighthouse?
-Why did the twins bring Booker back at all?
-The twins only notice the scar on his hand once they pull him through, there was no way they had time to create a whole campaign around "look for the false shepherds scar."
They have, but there is no problem with explaining again since it's understandable not everyone will read such a large thread.
First point, the lighthouse keeper. The Luteces murder him to prevent him murdering Booker. There is a note on the map alerting the lighthouse keeper that 'he is coming' (paraphrased) sent by "C". The logical conclusion to this is that Comstock sent the note so the lighthouse keeper would prevent the False Shepard making it to Columbia. The Luteces have a note in their laboratory which also alludes to them murdering him as their is a picture of the lighthouse that has 'but one problem remains' (paraphrased). Both notes were posted earlier in the thread so I'll edit this post later with the pictures of each. As for the brutality and notes; so that Booker does not flee to Paris with Elizabeth. Booker states that 'these aren't the sort of people you want to cross' (again, paraphrased) to Elizabeth.
Secondly, what do you mean? Why do they bring him to Columbia? A few reasons, all found in three Voxophones. The first (in Lutece Laboratory I believe) states that both Luteces become trapped in the timeline when Fink botches his murder attempt by sabotaging their machine. The female Lutece doesn't care because she's with her male counterpart. The male Lutece is unhappy with their predicament however. The second Voxophone states that male Lutece offered the female Lutece an ultimatum with regarding to resetting the timeline; either she accepts or they part and as we see them together, she accepted. The third shows that male Lutece was feeling guilt over their interference and wishes to reset their actions while the female Lutece sees it as pointless because 'time is like an ocean, why turn around a tide' (again, paraphrased). Again, I'll edit this post later to add the exact ones in.
Ultimatum: My brother has presented me with an ultimatum...If we do not send the girl back from where we brought her, he and I must part. Where he sees an empty page, I see King Lear. But he is my brother, so I shall play my part, knowing it shall all end in tears.
Scattered in the timeline: Comstock has sabotaged our contraption. Yet, we are not dead. A theory: we are scattered amongst the possibility space. But my brother and I are together, and so, I am content. He is not. The business with the girl lies unresolved. But perhaps there is one who can finish it in our stead.
Time is an ocean: Our contraption shows us the girl is the flame that shall ignite the world. My brother says we must undo what we have done. But time is more an ocean than a river. Why try to bring in a tide that will only again go out?
Note also how the final one also alludes to the machine being the source of the New York vision, not Old Elizabeth.
Third, is it said they only notice it? I think the female Lutece is simply struggling to understand, and asking about, the motive of it as opposed to simply noticing it. She is extremely nihilistic so this would further fit into her character, she doesn't see why he's bother to do it. The signs were almost certainly made by Comstock looking into a tear. I'll have to check if this is specifically stated anywhere but I think that seems like a logical assumption
I thought the Archangel was the Lutece twins? Weren't they simply manipulating Comstock in order to get what they wanted?
Yes to the first (the archangel figure was just propaganda to further bolster the personality cult by making it seem like he was chosen by God) but no to the second (or at least I doubt it). The female Lutece (which comes from Comstocks' universes) doesn't really care about anything and he provided funding (so she could eventually get her male version into her universe) so it doesn't seem like there was ever any manipulating to Comstock. They simply showed him tears which he used to predict what would happen. The Luteces' manipulating events seemed to only be to Booker, to get him to reset the timeline.