Do you believe you have an eternal soul? If you can at least believe this, all the other doubts can easily be removed. If you do not, then we have a problem.
"I keep going back to the fact that I am a soul within a body and I am incapable of fathoming myself as solely a biological being."
Because you at least have a foundation based upon knowledge that you have a soul, I can help build your faith back up that I think will make all of your doubts crumble.
You have an eternal soul. But there is a problem, isn't there? Something is not quite right... something is broken inside you. You understand what I am saying. This is the result of SIN which is a rupture between the union that is supposed to exist between our soul and God who created us. You were made for the Light... and yet you remain in darkness, fear and doubt. Why is this? The answer has a name and it is already on your lips.
If you look out into the world, you notice something is terribly wrong. People are killing one another, in fact, we have come to the point in society where we make it lawful to literally murder an innocent child (both in the womb and outside of it...) when it is so helpless and vulnerable. We are supposed to safeguard and protect the most helpless and innocent in our society, and yet we are literally HELL bent in destroying this life. Something isn't just WRONG... It is terribly, horrifically wrong. How can this be fixed???
This is where God steps into the picture. We are broken, weak, sick and something is wrong inside of us... so we CANNOT fix it. How can we have a sick surgeon who is blind and lame fix somthing broken? Not only will we fail to fix it, we will inevitablly make the problem worse. God is the Divine Physician... He comes to heal the sick, to proclaim liberty to captives, to give sight to the blind, to cure the lame, to literally bring the dead back to Life.
But how does He do this? To fix something broke, to heal, to restore... there has to be price paid... a sacrifice. A fall from God who created us demands a heavy price. Do you know how much your soul is worth in God's eyes? The price paid is the Blood of His only Son. This is how much was paid for our debt. And yes, God who created you as His child, loves you so much that He did send His only Son to die for you so that you may have Life.
We broke it but could not fix or pay the debt in our human nature. Human nature was responsible, but there is nothing we can do to repair it as the amount is incalcuable. Only something infinite..without limit could pay it... repair it... again we are dealing with a broken eternal soul that has been left in darkness as a result of sin.
Again, this is where God steps into the picture. God the Father sends His only Son to "take upon Himself" our broken and sick human nature. He "robes Himself" in flesh in order to pay the debt that we owe. He did suffer, die, and was buried. God pays the debt that we owe and pays it back with the same instrument that orginally caused this great, Hell-bent destruction within each one of us... our human nature... with His own Blood.
Please listen to the words of the Prophet Isaiah God sent among us way before this plan came to be fulfilled:
"And he shall grow up as a tender plant before him, and as a root out of a thirsty ground: there is no beauty in him, nor comeliness: and we have seen him, and there was no sightliness, that we should be desirous of him: Despised, and the most abject of men, a man of sorrows, and acquainted with infirmity: and his look was as it were hidden and despised, whereupon we esteemed him not. Surely he hath borne our infirmities and carried our sorrows: and we have thought him as it were a leper, and as one struck by God and afflicted. But he was wounded for our iniquities, he was bruised for our sins: the chastisement of our peace was upon him, and by his bruises we are healed. All we like sheep have gone astray, every one hath turned aside into his own way: and the Lord hath laid on him the iniquity of us all. And the Lord was pleased to bruise him in infirmity: if he shall lay down his life for sin..." (Isaiah 53:2-6,10a)
I think your eyes have been opened enough by now to see with the eyes of Faith. The rest of your Catholic Faith lies upon this foundation. God is very real... and your state of sin and darkness of soul can detect this now. If not... you are doomed.
"Every one that cometh to Me, and heareth my words, and doth them, I will show you to whom he is like. He is like to a man building a house, who digged deep, and laid the foundation upon a rock. And when a flood came, the stream beat vehemently upon that house, and it could not shake it; for it was founded on a rock. But he that heareth, and doth not, is like to a man building his house upon the earth without a foundation: against which the stream beat vehemently, and immediately it fell, and the ruin of that house was great." (Luke 6:47-49)
I think the above will shake your doubts to the core and make you realize that logic can only go so far... there is something else that has to take you out into the Deep. It is called Faith.