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*** How do you know the Bible is a product of the Holy Spirit? How do we know the Gospel of Thomas was not?***

We know it because of the witness of the early Church to the presence of the Holy Spirit in those books. Here is an example used by the Church Fathers...

John the Baptist was granted the privilege of recognizing and publicly proclaiming the Messiah. He was told it would be the one on whom he say the Spirit resting.

The same is true of the early Church. They were given the privilege of recognizing the authentic Scriptures.

But John the Baptist did not have the ability to confer any authority on Jesus. He did not have the ability to decide whether Jesus was or was not to be Messiah - neither did he "make" Jesus the Messiah. Jesus was the Messiah - God's sign was the presence of the Holy Spirit over him. John was given the ability to recognize that.

Similarly, the early Church did not have the ability to confer any authority on the NT Scriptures - the Scriptures are inherently authoritative. The early Church saw the sign of the presence of the Holy Spirit in the Gospels and Epistles and proclaimed them as the authentic Scriptures.

But you are trying to infer from the above that the Church therefore is somehow "over" the Scriptures and in so doing you seek to enhance the authority of the Church and decrease the authority of the Scriptures.

John the Baptist was subject to Jesus and called him "Lord". Even so, the Church is subject to the Scriptures - for it is the very Voice of her Master.

But you are trying to infer from the above that the Church therefore is somehow "over" the Scriptures and in so doing you seek to enhance the authority of the Church and decrease the authority of the Scriptures.

You imply that the Bible is somehow "over" the Church and the Church is somehow subject to it. If the Church has always been subjected to the Bible, what were the early Church fathers subjected to before the Bible even existed? Apostolic authority.