I can see why you believe what you do about the spirit and this I am sure won't change your thinking.
Here it is anyway.
This scripture says that God is a Spirit.
Jn 4:24
God is a Spirit: and they that worship him must worship him in spirit and in truth.
KJV
God made man is his image and likeness.
Ge 1:26
And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth
KJV
We agree, I am sure that the Godhead is a trinity.
God made man in his likeness and image he made man spirit, soul and body.
1 Th 5:23
And the very God of peace sanctify you wholly; and I pray God your whole spirit and soul and body be preserved blameless unto the coming of our Lord Jesus Christ.
KJV
Mary at the time of this event was not a born again Christian as Jesus had not gone to the cross yet. Therefore the Holy Spirit was not residing in her yet.
Notice she is aware she is spirit and comments on it.
Lk 1:46-47
46 And Mary said, My soul doth magnify the Lord,
47 And my spirit hath rejoiced in God my Saviour.
KJV
When this maid was raised from the dead her spirit which is the place of life came back as Jn 6:63 also shows.
Lk 8:54-55
54 And he put them all out, and took her by the hand, and called, saying, Maid, arise.
55 And her spirit came again, and she arose straightway: and he commanded to give her meat.
KJV
Jn 6:63
It is the spirit that quickeneth; the flesh profiteth nothing: the words that I speak unto you, they are spirit , and they are life.
KJV
And when Stephen died his spirit(him) went to the Lord.
Ac 7:59
And they stoned Stephen, calling upon God, and saying, Lord Jesus, receive my spirit .
KJV
When the spirit leaves the body so does the soul as they are connected.
Heb 4:12
For the word of God is quick, and powerful, and sharper than any twoedged sword, piercing even to the
dividing asunder of soul and spirit, and of the joints and marrow, and is a discerner of the thoughts and intents of the heart.
KJV
The word can divide them which is the only thing the word mentions that can.