Time traveler souls
I propose the following: Souls are time travelers.
A soul can reincarnate in a body that is born in the past respect to the moment of death of the previous body. That is, when a person dies, its soul could go to a new born in the past.
Thus – assuming souls have identity – there could be two bodies in the same time period that are being occupied by the same soul, except one of them is an early version, and one of them is a later version.
Furthermore, there could be only one soul per species, and without any need of soul fragmentation.
Oh, and before you consider it... No, sex is not part of souls… some species can change sex midlife.
This is a possible framework for what I suggest above
You say souls have energy. However, it appears souls do not have mass. If this is true, free souls (souls not attached to a body), would move at the speed of massless objects (the speed of light). If this is true, in the frame of reference of the souls time does not pass, that is, all instants are the same for the free soul. This also means that souls do not need bodies, nor do they experience the time outside a body.
I also want to bring a philosophical interpretation of Feynman diagrams… these diagram represent particle interactions, with one of the axis of the diagram being time. However, these diagrams remain valid when rotated, except that when you rotate them half turn, what used to be electron is now a positron (and vice-versa). Under this interpretation, a positron is an electron traveling backwards in time from your frame of reference (and vice-versa). Going further, there could be only one electron/positron that travels back and forth in time, and as a result all electrons/positron are the same.
Note: electrons are indistinguishable from one another, same for positrons… and any fundamental particle actually.
Then why electrons – and other particles – have the particular properties they have? Well, because there is only actually one of each, and this is how they were created.
I am suggesting that souls behave similar to that, traveling back and forth in time. Why a soul is of a particular species? Because that is how they were created (or how they always have been, if your cosmology has no creation), along with the universe.
Conservation of energy and time travel
Evidently the soul won’t be like the electron (electrons have mass and have a distinct antiparticle), but like photons (that have no mass and are their own antiparticle). Thus, a soul is a soul going backwards or going forward in time, it makes no difference for the soul.
Yet, photons have energy, if they go back in time, won’t that mean that a moment in the past would have more energy than one in the future?
Well, these particle that go back in time are virtual particles. They are only one of the infinite paths that particles take in an interaction. Under Copenhagen interpretation, particles go into a superposition of all the paths, including those that go back in time… and these can break conservation of energy. However, when the particle interacts with another, it collapses in such way that the interaction respects conservation of energy.
Souls would be like that. When free from a body, they go into a superposition that can break conservation of energy and time travel. However, to enter a body, there would be an interaction with it, such that conservation of energy is preserved.
Thus, if the soul adds energy to the body, some energy must be lost. In fact, under the assumption that the body-soul link is in stable equilibrium, it must be a low energy state, thus it makes sense that energy is released…
Yet, it cannot be released to the environment, at least not at the time of linking (that would still result in more total energy in the universe), instead, it must be released to the time from where soul comes from. Well, the soul comes from the body of the prior incarnation is dying.
Thus, in time A: some energy is lost because the soul leaves, the dead body. Then the soul goes to another time B. In time B: the soul links to the new body adding energy. In consequence equivalent energy leave the body and is send to time A. Then in time A: that energy is released.
Consequences: conservation of energy is preserved, and the energy release when the soul leaves the body could be detectable. In what form is that energy released? Use your artistic license. Addendum: Scientis could think that that is the soul, it isn't. Perhaps this is an excuse for ghosts if you want them in your setting.
These are some ideas on the biology of species tied souls
Perhaps souls species needs some wiggle room. As we know individuals of the same species differ biologically. Yet, they would all be viable vessels for the same soul.
If scientists create new variants of a given species, souls could still populate these bodies.
However, perhaps a body is that has mutated too much could not host a soul.
If scientist create a new species – out of genetics and bio-engineering – these might or might not host souls depending on whatever or not they are a close match for existing species.
Why would a body need a soul? If we need excuses for souls as postulated here, I would say that souls shape the growth of the body. In that way there is rational link between the species of the soul and the species of the body.
This would also suggest that if the attachment of the soul to the body is not ideal, the body may have uncontrolled growth, I mean, cancer. From another point of view, if the DNA of parts of the body is damaged in such way that it does not match the species of the soul, the attachment of the soul to the body would be severed, preventing it from shaping its growth, leading to cancer.
An interesting consequence of this idea (if you choose to allow it in your setting) is that if you could, by means of science or magic (again, if you allow it in your setting), force a soul into a body, that body would start to resemble the species of that soul. This also opens a backdoor for chimera creatures, lycanthropes and such.
About the moment the soul enters the body… I would say that it happens at some point between the conception and the first cell division.
This also imply that eggs do not necessarily have souls by themselves.
Ah, and I would remind you that there are some virtually immortal cancerous human cells that are used for research (HeLa). Under my proposal, her soul is not trapped there.