It is important to understand the difference between scientific hypothesis, such as "Humans are descended from animals that lived millions of years ago," and metaphysical truth, such as "The first humans were created miraculously, with no ancestors, a few thousand years ago."
Nothing in science can be said to be true, in any fundamental sense. Consider: any scientific hypothesis/theory is falsifiable, meaning, we must always allow that it could be disproved. Newton's theory of gravity is a perfect example: it's wrong, and we've known it's wrong for over a hundred years. Einstein's relativity could also be wrong. Nothing that could potentially be proved false can be called truth. A hypothesis/theory is a proposed explanation for what we observe, not a truth-claim.
We use science because it is useful; the truth of the underlying reality is irrelevant. For all we know, from a scientific standpoint, we could be a computer simulation. From a scientific standpoint, there would be no way to know. Science cannot tell us the truth about reality, and it cannot prove anything.
The Qur'an, the Bible, all holy books, and all religions are not about hypothesis or theory. Religions are about truth. They do not provide explanations, but rather make truth-claims, that is, assertions. For example, the assertion that Adam and Eve were the first humans. It is not an explanation. It could be considered an answer to the question, "where do humans come from?" But it's not an explanation in any scientific sense. As mentioned above, a scientific explanation is open to falsification; a metaphysical assertion is not. Any apparent disproof of the Adam and Eve assertion could always be met with another assertion, perhaps that Shaytan and the Jinn planted the human-like fossils to lead mankind astray.
Science and metaphysics are two fundamentally different endeavors. The only answer to your questions, from the standpoint of Islam or any other religion is, "God knows."
