You have obviously put in a lot of effort trying to express your belief in evolution using a Christian metaphor.
While the phrase above expresses an idea, it lacks precise meaning. Obviously, “man” did not actively develop a conscience. He would have been a passive recipient of a “conscience”. The word to me represents our internal dialogue with God, the Good, Love. As such it usually involves His reaching out to us, as He did in the story of Cain. That relationship must pre-exist, which is to say that there needs be an aspect of our soul that includes free will and the capacity to know. We cannot be instinctive creatures, perceiving, understanding and behaving in a preset, determined fashion. So, the suggestion that we may have chosen to have a conscience runs into trouble because it presupposes that a conscience must already exist. There could be no warning not to eat it because we eat what we would have been programmed to eat.
Let’s assume that animals were given spiritual souls à la Aslan in Narnia, where he creates that world giving speech and reason to pairs of animals. This would involve a transformation of a primitive purely material soul into an eternal one. As the core reality of what anything is, I don’t see how it is possible for one soul to become another. It would be like you becoming me. If we consider an embryo or zygote as simply a collection of cells, it could be that a soul is bestowed on them, created as it were using living matter. The genetics and associated processes may have been tweaked to produce a larger brain. Alternatively, the desire of greater intellectual capacity may have driven ape-like creatures to instinctively prefer mates with characteristics that approximated that eventual ideal. Again, the mass of cells arising from a specific couple could have been ensouled with the spirit, the breath of God. The way I see things, what exists does so as a unity. Each kind of living being is capable through God’s gift of life, to reproduce itself; there is no actual ensoulment after the first and animal forebears mankind would produced animal offspring from the embryonic stage onwards. The bottom line is that it boils down to a belief, which if true, would have been stated in Genesis.
I don’t understand what exactly the Pope was talking about stating that mankind could have been created using living matter. It sounds like he is trying to reach a compromise, accepting that it is not necessarily idolatry, worshipping the world as creator of mankind, to believe in evolution. Those who accept it blindly are in a different position than those who advocate for it however, and the latter should reflect on how their beliefs may conflict with those of the church.