Wow, lot’s of questions that cannot be answered simply and certainly not in one post. For starters I would suggest getting (and reading) a book called “Theology for Beginners” by Frank Sheed.
The words “soul” and “spirit” are often used interchangeably (even in the Bible), but they are slightly different. All living things (plant, animal, God, angels, etc.) have soul. It is the principle of life. However, rational beings (humans, angels, God) have soul which is also “spirit”. Spirit is what gives us the capacity to know, love, and will (as opposed to animal or plant soul). As the scriptures say, “God is a spirit” (John 4:24). And also as the scriptures say “And I will set my tabernacle among you: and my soul shall not abhor you” (Leviticus 26:11).
With that in mind, the cornerstone the builders rejected was their Messiah, Jesus. Not a part of him (the soul), but all of him in his personhood as divine Son of God. Spirit is eternal, but soul is not. God is a spirit, Angels are spirits, humans have spirits, but we are not the same spirit. I do not love what you love. I do not know what you know. Neither of us have the knowledge, love, or will that God has. We all possess an individual spirit, thus they are not the same.
Jesus is a divine person who took on humanity. We have seen the Father when we see Jesus because they are the same God (but not the same persons). You and I are both human, but we are not the same person. Jesus, the Father, and the Holy Spirit are the same One God, but they are not the same persons. They know, love, and will with the same oneness of God, but they are not the same persons. To know the love of Jesus, is the same as knowing the love of the Father and the Holy Spirit. This is a divine mystery. We can sort of understand it, but at the same time total comprehension remains a mystery.