> How did "Original Sin" get passed to all other humans?
The Bible doesn't tell us that. It can't be strictly biological, because the Bible teaches that Jesus was sinless, and yet was fully human and had a human mother. Some had speculated, then, that "original sin" is passed through the father, but when it comes right down to it that doesn't really make sense.
It has to be more of a spiritual thing. When A&E sinned as representatives of humanity, they, and all humanity with them, became separated from God (separated from Life), and therefore "dead" in their sins. An analogy might be that if your parents gave up their citizenship and moved to another country and became citizens there, all of their offspring (theoretically forevermore) would be citizens of the new country, not of the former one. When Adam and Eve chose to renounce their citizenship in God's kingdom, so to speak, they became citizens of the kingdom of the world, and with them all their offspring.
> Were there soulless humans that were in every way as conscious (same capacity to perceive each other), self-aware (demonstrated by death rituals going back tens of thousands of years, and painted hand-prints much older) and intelligent (same brain) which coexisted with specifically the descendants of Adam and Eve?
There may have been soulless hominids—that's the way this interpretation of the story rolls out. But the time frame of tens of thousands of years back is irrelevant. No era is given for the Adam and Eve story. It may have been that long ago. But these other hominids, by scientific guesstimation, probably didn't have homo sapien sapien capabilities.
> How did God's punishment specifically of Adam and Eve not already exist?
Which punishment? The ones after they sinned? Those, by definition, were post-sin, not "already exist," so I'm not sure I understand your question. There were no punishments pre-sin.
> Why does every genomic study of human origins and human migrations completely discount there ever having been a progenitor couple?
The human family tree is being repeatedly redrawn as new discoveries are made.
Try checking out "Mitochondrial Eve" at
http://en.wikipedia.org/wiki/Mitochondrial_EveBut all of this is far from being decided. New discoveries are remaking the landscape with regularity.
> One. Not two.
The term "adam" in early Genesis has two references. When used without the article it generally refers to a personal name. When used with the article it speaks of humankind. Gn. 2.7 and 15 both have the article. It's talking about humanity, not a guy.
> God performed surgery on Adam in order to clone a woman from a rib
No, you have this all wrong. They knew nothing of surgery, and that's not what the text is about. The "deep sleep" is a vision, not anesthesia. The "rib" is not an anatomical word elsewhere in the OT (a very unfortunate translation). It's more of an architectural word, and therefore speaking figuratively here. This text is not about Eve's material origin, but God is communicating to Adam about the nature and identity of the woman to whom he is about to introduce him.
> If there were other people, why choose a bachelor (to create from dirt), and not choose a woman?
The "create from dirt" is not a statement of material origin, but of humanity's mortal nature. See also Gn. 3.19; Ps. 103.14.
I'm trying to be brief here, so I don't write a wall. There is so much more to say, and you've asked many questions, but there is only so much space. My answers here are greatly abridged, and not all that has to be said.
> This completely contradicts the existence of the fruit of the Tree of Knowledge.
It doesn't at all. I'm not making things up. The tree of Knowledge represents man's free will and his need to choose to love and obey. It was still a literal tree, but was vested with significance. We say, "The White House said..." Well, we all the White House didn't say anything, but it represents what the President and his staff report. When I draw a line in the sand and dare you to cross it, the line is virtually meaningless, but on the other hand it represents our relationship. That's what the tree was.
> nd in fact, paraded every animal past Adam, so that he could name them, and he could have dominion over them, which contradicts there could be any other humans.
Not at all. You're not reading carefully. In Gn. 1.27-28, all humans were given the authority to rule and subdue. All humans. And you'll notice in 2.19 it's "the adam" (definite article), indicating that all humanity is involved in the study and categorization of life. We do this with our Kingdom/order...genus/species system. We're STILL doing it as new species are discovered. It's not a contradiction at all.
> relationship
The whole Bible is about having a relationship with God. Gn. 4.26; 5.24; 6.9; 12.1-3 etc etc., all the way in Philippians 3.10 and others.
> why a relationship with two specific humans from multiple species of humans
They were ready. It was the right time and the right development.
> why impose punishment on all humans based on the actions of the single one God made??
Refer back to my "citizenship" analogy. But also this: God doesn't impose punishment for all of us based on the actions of the single one. You and I disobey all on our own. We're as guilty and rebellious as they were. Don't think God is punishing you for their sin; he is punishing you for your own.