I can offer some possible answers to some of these questions. They are not the last word or even everyone's answer to the questions raised, but they might help you find answers if you are willing to look beyond your present views and ideas.
Why did the Jews “kill all their enemies, men, woman and children - but not the virgin girls”?
The stories you read in Scripture are propagandized, meant to read a certain way to ancient minds using ancient narrative devices. To claim in the Bible that "all the enemy was killed" and that the best of spoil was carried off, whether it be gold or livestock or virgins, was a way of attributing glory to God in ancient terms. Note how this is also done when describing God sending plagues upon Egypt: the 5th plague kills ALL of Egypt's livestock (Exodus 9:1-7), but then God kills the same animals again with a hail storm and fire (Exodus 9:13-35), and if that is not enough, though ALL the animals have been killed at least twice, the firstborn of all the animals die in the 10th and final plague (Exodus 11:1-12:36). And somehow, after all this, there are still dogs left to be silenced by God as the Hebrews leave Egypt, and horses for the enormous army of Egypt to draw their chariots in pursuit of the escaping Hebrews! All this after the Bible claims the Hebrews stripped the Egyptians of all their precious goods--which would have included things like chariots as these could have been used to help transport all the spoils of Egypt. (Exodus 11:7; 12:36; 14:9) No, this type of language is not literal. It is just an ancient way of describing how powerful God is against Israel's enemies, even if the actual events didn't happen just this way.
Why [did] the Jews slaughtered cattle, birds and other animals and burned it in the temple of Jerusalem?
While many Christians might have you believe this was a unique system designed to provide a means to appease God with the blood of sacrifice, it was really the way all ancient communities butchered their meat. The process of the ancients went like this: animals could be eaten as long as the gods of the people were thanked for the food; if the community had priests, the animal was slaughtered and the blood offered to the gods in the butchering process; some meat was given as a gratuity to the priests for their butchering skill. The Mosaic Law allowed the Jews to have a similar system, only that in their case God allowed for liturgical ritual butchering to also be means of asking forgiveness for sins. It was not the only way sins could be forgiven, mind you, but it was also available for you when you went to get your meat butchered. This explains why the early Christians had issues about eating meat purchased from pagan markets as the pagans butchered their animals in similar rituals as an offering to their own particular gods.
Why did the people of God actually accept and encourage the habit of taking slaves?
Slavery was a facet of all ancient Mesopotamian cultures, a norm, and the ancient civilization of the past unfortunately created a world that depended upon it. The Mosaic Law did not introduce slavery, mind you, but it did regulate it. It also encouraged the releasing of slaves whenever possible. It curbed the way slavery could be carried out among the Hebrews as to avoid the inhumane treatment carried out by Gentiles upon slaves.
Why did the Christian God have to torture and kill his son to be able to forgive his other creations?
Christianity does not teach that God required the sacrifice of his Son to forgive humanity. What it teaches is that God came to humanity in order to offer his life as a sacrifice for the world. God does not need blood or the life of other people. The Christian teaching, though it differs greatly with the Jews, is not entirely illogical. As Jewish sacrifices were not merely ways to gain forgiveness but to obtain food for everyday life, the sacrifice of Jesus is supposed to be the ultimate sacrifice that offers not merely forgiveness but the "food" that grants "eternal life" for the humans that 'eat of it.'--See John 6:27-35.
Why did a loving caring Father and God, let almost all of his children drown In a flood?
He didn't. The Noachian Deluge is a Mesopotamian cosmological paradigm that was one ancient explanation of the origin of the universe. The ancient Mesopotamians believed that there was no vacuum of space, only a vast eternal sea. The majority believed that life sprang from the sea, and some believed the current world came from a previous world that was erased by the waters due to humanity being "wicked." The Hebrews merely adapted and employed this paradigm in the story of Noah, as one of three cosmological origin myths that appear in Genesis (the other two appear in chapters 1 and 2). Noah may have been a historical figure who survived one of the many Mesopotamian deluges that often wiped whole villages away on a regular basis, but the story was altered to fit the cosmological origin narrative. It is not a historical report.
Why do Priests, Monks and Popes, let female creatures burn up in fire because they think they are obsessed by the devil?
While some Catholics have done horrible things to people (including my own, being that I am Jewish), it had less to do with them being Catholics as it had to do with them being unfaithful Catholics. Some atheists have been just as horrible at times. When the concentration camps of the Holocaust were liberated by the Soviet armies, at night the Soviet soldiers (who were atheists) would rape many of the women prisoners even though they were starving, ill, and near death. Many of my aunts and grandparents suffered like this before the Allies came to free them. But this does not mean all atheists are evil. On the contrary, most atheists are very good people and I have a blessed life by having many as friends. The same go for Catholics and people of other faiths.
People do not require religion, a belief in God, or the Scriptures in order to act objectively moral. The opposite is also true: immoral, unjust acts are not the exclusive acts of the religious. The non-religious carry them out as well.