Here's my theory regarding the comet birthmark. I believe that the people who have the comet birthmark in the film, aren't the same soul reincarnated, but are actually different souls that have their turn to play a particular, important role in that time of the human history. There is a connection between these people, through time and space, and in the end, this connection, is ultimately a journey of humanity into another world.
The first one to have the birthmark is Ewing. He goes through a personal adventure, in which he has to make an important choice, that will in turn save his life, as well as make him a kind of a hero in his time. He will choose to save Autua, who will in turn save him, and this experience will make him decide on what is the important role that he has in his life, which is, work for the abolition of slavery. Our lives are not our own - his life, after a very important meeting, he gives it to an important cause, which is the most important cause in his Epoque, of people fighting against the Establishment, and those who do not want to mess with the Natural Order (the characters played by Hugo Weaving, Hugh Grant). He writes a Diary, which becomes a book about his adventures.
The second to have the birthmark, is in fact Frobisher, who reads exactly that diary. In some sort of cosmic, time-crossing kind of way, Frobisher's and Ewing's lives intertwine. It's some sort of rite of passage that Ewing gives Frobisher to continue his adventure. Frobisher is in love with Sixsmith, and throughout the film we see him connect with Jocasta and Vyvyan, but I don't think any of those loves are what he's talking about in his suicide note. I think he's talking about a far greater love, that is his sextet, his music, his creation, that he knows deep in his heart, it's far greater than him, far greater than life, it's in fact the story of all these people meeting again and again in different times, and through their choices, shaping the future of humanity. It's in fact the music of love that connects people to fight for a better world, and for the continuity of all that's good in human kind, that kind of love. Sixsmith, it's his inspiration, his soul mate if you will, and the cloud atlas sextet is his poem about this love, that transcends all time and space, love he has for Sixsmith, but also the love of all these souls that shape humanity.
Frobisher creates this magic music piece that is a mathematic, musical, and time-infinite expression of the human adventure in different periods of time (considering that time is infinite, past, future and present, are all happening at the same time in the immense universe). The music he creates, I'm sure Vyvyan Ayrs might have dreamt it, getting a glimpse, a window opening of the future, in the dream about the waitresses with the same faces (In the Somni time period), because it's timeless and it represents all of them, but he, unlike Frobisher does not understand it. He wants to own it, he doesn't care about the rite of passage (We are all meeting again and again in different times), he cares to make a name out of it. But Frobisher knows the importance of life after death, he doesn't care that there is no way he can have a successful life at his time. His most important duty is to create this piece of music, that he knows it's important, as it is an anthem to something far greater than him, this cloud atlas sextet is a musical description, summary of all the connections between these souls who antagonize or love each other in different times, but together have ultimately an important role in human history.
As a matter of fact Frobisher sends the letters to his one true love Sixmith, describing his adventure, and he also creates this masterpiece. And who else but Luisa Rei, the next carrier of the birthmark would ultimately come across these letters, and also the music? She knows she has heard the music piece, not only because she was Ayr's wife in another life, but because this music is about her, as it is about all these souls, and all their incarnations, and she knows that the music is important. Sixsmith knows and feels that his meeting with Luisa is important after seeing the birthmark, that is why he is sure to contact her and trust her with his important task. Luisa comes across the letters, she feels that we all make the same mistakes over and over again, she feels that those letters are more than the story of one person, but they are repetition of the human experience which happens again and again and again, and that she was ultimately meant to read them. There's a reason for everything, and if our rational brain cannot comprehend our role in this world, something more than a birthmark shows us the way, an instict. After all maybe the mind unlike the human body is connected with everyone else and everything else around the universe, across all time and space in ways that we cannot really comprehend, stapled on this material world. Luisa was meant to read the letters, just like Frobisher was meant to read Ewing's book. She is inspired by the letters and ultimately by the music to carry out her part of the deal, her rite of passage in fighting the evil, the natural order, passing the limits, the challenges, and winning human freedom, by saving thousands, or hundreds of thousands of lives, in her adventure to get the research about the nuclear power public. Hugh Grant and Hugo Weaving are again the protectors of the evil, and the natural order. And we see Tom Hanks' soul-character, Isaac, for the first time come to his senses and see and meet his soul mate, which he has met in past and future (remember time is endless, it's not linear, it's cyclical). Through this meeting he is convinced to make an important choice, he was afraid to make before. This meeting inspires him to give Luisa Rei the research, before he is killed. He knows when he meets her, that something far greater than him was happening. Luisa Rei's story as we are led to believe by her conversation with the little spy novels loving kid as they read her expose on the paper, was most probably going to be made into a book.
Again, my theory is that Cavendish is reading exactly that book. he is connecting with Luisa Rei through her book, and as we are let to know he is the carrier of the birthmark (it's in his leg). I don't think he is a reincarnation, he was probably born when Luisa Rei was still alive if you do the math, but that doesn't mean that there's a plothole. Again I don't think they are reincarnations, I think they are important chess stones that play their part in this grand domino effect, and if you are just a little bit spiritual, intelligent design. Cavendish goes through a little adventure of his own, where he has to pursue freedom against the people who want to take it away from him. He has to live through the incarceration, because that is important for the grand scheme of things, of destiny. His little experience will inspire him, to write a book about it, a book, that was ultimately made into a film. His role was exactly to make that film.
The other carrier of the birthmark, is Somni. We see that when her collar is taken off from Halle Berry's Asian male character. Somni is inspired by Cavendish's film, it is her first realization that she doesn't have to be incarcerated, abused, that she is human, free, and thus her journey to be part of the revolution and tell people of 2144 that clones are humans too, that our lives are not our own, that we play part in the life or lives we have by the connections we make, the people we meet. Yes we are all in fact drops that make a multitute of the ocean. It is only together that we make the whole. That is why the connections that we make are important, because together we are fated to create our unique, universal and shared destiny. Somni is captured ultimately and killed, but she is able to tell her story and register her message in so many places. She is sure that when we die we close a door and open another, and we can meet again and again in different time periods and different incarnations. Somni's role is important. Her message is registered as I said in this tower. Ages later after a sort of apocalypse has fallen upon humans and the earth has become little by little a harsher place to live, her message was there. My theory is that the people of the Valley where Zachry was from, their ancestors had seen that message, and that it was passed from generation to generation until people thought Somni was a deity. (If you see carefuly the same place where Somni was captured, is the place where Zachry and Meronym go to send the message to another planet, another star).
As we see in the end Zachry has the comet birthmark this time (his balding head as an old grandpa). His role was prominent to save Meronym, to send the message, to assure that humans would continue to live on and not be extinct, to ensure that humans could pass on the gene-line of generations and generations past (there are more ways to reincarnate, I believe that the DNA and not just the energy-soul, where the information of our ancestors is stored in us, is important for the humanity to continue, and for the story of human kind to continue). Zachry and Meronym are able to go to this new land, this new planet, where in fact a galaxy of stars seen by that planet, looks in shape a lot like the comet shaped birthmark Ewing, Frobisher, Luisa, Cavendish, Somni and Zachry have. It was in fact a map of the new world Frobisher was talking about (I believe we'll meet again in a new world). And I don't really know how it may continue, whether others' souls of this map of people-souls entrenched together can also now reincarnate in this new world, through the energy, or through gene-line, but I do feel that the journey of one human, is the journey of all humanity, and all humanity was meant to travel to this far away galaxy and continue our existence in a new world. The important part is that human kind, through this domino effect of events of the people who held the comet shaped birthmark, was able continue its existence in another world, that the birthmark had described. Who had the birthmark, had the most important role in that particular time to make something important in their generation, that would inspire the next generation's person with the birthmark to do the same, thus ultimately having Zachry send Meronym to the mountain and have the people from outter space come and rescue us.
So as a summary - Ewing had the first birthmark, he had an adventure that changed his life and destiny, he wrote a book about it, that was read by Frobisher who had the birthmark, who was so inspired by him, that he created the beautiful music and wrote about his little adventure to Sixmith. Luisa read those letters, and she knew they were important, she heard Cloud Atlas because of it and she knew it was important, she had the birthmark, she had a great adventure to save people, she wrote the story and the book about it. Cavendish had the birthmark, and read Luisa's book. Was he probably inspired by it to want and pursue a life of freedom, and even write himself? I think so. He knew it was important that he wrote the story, the book, and that it was made into a film, and that film was watched by the next person with the birthmark, Somni. Somni was inspired by the film to make her revolution and leave a message of the connectedness between humans, and how important our lives are to give them to the people next to us. Zachry who saw her first as a deity, and followed her preaching, and then saw her message in the mountain playing, knew his role to help Meronym, and made the right choice by helping out Meronym, and thus played his part into saving humanity and sending them to this new world.
What is an Ocean but a multitude of Drops. We are all drops of this human multitude, we connect time after time with each other. Every meeting we make, turns our life in a certain direction. Perhaps the choices we make, we were meant, or written to make in the first place, but we still have to make those choices, and play that part to make it all happen. What is all? It's our history as humans, our history as beings, conscious on this earth. Maybe there's more than just us, but we, as small as we are, we do have a role to make it all happen, all that is supposed to happen. It's our role to fight against what our enemies, suppressers of freedom and love call the natural order. If it feels right, if it feels that we have a duty to do something, a mission, to play our small part in this world, to make it better, that is our part to play, and we should give our lives to that part. Our lives are not our own. We belong together on this earth, in this universe, in this multiverse. That is what Cloud Atlas inspired me to, and all of us, even though we don't have a particular birthmark, a rite of passage to ensure humanity's travel to a better world, we still are chess pawns, in a good way, in this grand intelligent scheme, in this grand cloud atlas. So if there is a lesson to be learned, from this beautiful piece of art, to me, it is, make sure to live your mark on this earth, someone will follow your steps, to continue the journey, and that is how we become immortal, by being part of humanity's lineage, by being part of humanity's Ocean.