I'm not sure where even to start. Genesis 1 says that in the beginning He created the heavens and the earth. So granted God created everything ex nihilo. That question is admittedly outside the scope of science as we know it, so again I see no conflict. The Bible teaches that God made man from the dust of the earth.
Evolutionary theory traces the ancestry of man through early hominids back to primates.
So again I see no conflict. In fact you've spent quite a bit of time and effort showing that the flooding of the Mediterranean 5.5 million years ago answers quite a few geological conundrums about the flood account, and gives us a view of ancient man that says some interesting things about the question of what man is, if it's correct.