As I stated, the brain is the receiver of consciousness. It's the interface between the physical sensory organs and consciousness. You are talking about an issue with the hardware which impairs the flow of information to and from consciousness. The problem IS a physical problem. It does nothing, however, to prove the brain is the prime and lone vehicle of consciousness
Information comes from conscious individuals. To say that consciousness itself is created independently from the brain requires a greater explanation than the human brain itself. Evolution presents a simple, explanable origin of the brain and potential organs more complex from the first cell. The origin of consciousness would need a similarly simple explanation or you would have created an infinite regression of complexity (the creator of consciousness must be more complex than consciousness...)
I'm not going to get into evolution because it would be too much work just to state my perspective on it, and your question requires I accept the mainstream interpretation which I do not. What's more it is much too dependent upon speculation about what cannot be proven one way or another.
Would be interested in hearing your thoughts(I'm in college studying Evolutionary Biology, so a nice discussion would be enjoyable. Message me if you want.
But as far as individualized vs species souls you need only go back as far as the indigenous tribal cultures which anthropologists and psychologists, such as Heinz Werner, found lacking a sense of separateness from family/community, objects and nature. It could be suggested spiritual individualization bares a direct link to development of Ego. Early twentieth-century anthropologist Lucien Levy-Bruhl stated that the essential characteristic of native peoples was their less "sharpened" sense of individuality. He noted their sense of identity was bound up with their community and they spoke as "I" when describing the group. You can see a distinct trend during the last millennium away from groups and toward individual states of being. It could also be suggested the Abrahamic religions mark the point at which Ego was realized into the human experience. They represented a break from nature, including shame of one's own body and sexuality.
I haven't heard of this, but it sounds really fascinating, I'll check it out when I get time. Thanks! 
Your value judgments are based on emotional value and emotion is not physical but metaphysical. That's the main premise I was trying to get across. Your presumption that emotions are the product of sophisticated minds is only a presumption and with no scientific basis. I'm not saying a scientist wouldn't agree with you. They have a vested interest in everything being reducible to physical causes since science can only observe physical interactions. I'm just saying there is no definitive evidence, which would be important when arguing from a scientific perspective
Just because there isn't evidence for or against something doesn't make all opposing explanations have equal merit. We have an explanation for the hardware of the human brain and can (and will be able to do so better in the future) show the physical properties of emotions in the brain. positing a new explanation for emotion and thought just because we can't disprove it seems unnecessary, in the same way that me saying "Invisible Leprechauns are the true source of consciousness in humans" would be unnecessary.
You feel emotions and your endocrine system responds by releasing the chemicals that create the physical effects associated with that emotion. You suggest the brain calculates the emotional response making is physical yet in many cases emotions are very detrimental to survival and or rational behavior. Examples: Many people break down when faced with emergencies or risk their own safety (and that of their DNA) in order to save the lives of others. In that case do you think the brain works against itself or that perhaps emotions are not merely a mechanistic response to input data calculated by sophisticated minds? Regardless of our conclusions it could not be realistically stated that emotions are physical rather than metaphysical. Therefore, against your better judgment, you do feel a metaphysical connection to all life, and that's a beautiful thing.
I would say that "feeling" emotion is the response of the endocrine system. If there were a way to inject the right chemicals into a person and duplicate the feeling of a particular emotion, would that disprove your assumption that emotions are from a source outside of our physiology? And if not, what could disprove your assumption?
