So when reading scripture we should eliminate part of the scripture that doesn't fit?
It is kind of funny, because the church takes John 6 literally, because that fits your doctrine, but when it is convenient it is not
We read it all, but we understand metaphore when metaphore is used. The eagle wing passage also applies to Mary, like the door passage applies to Jesus. It is most likely a reference to her assumption into heaven.
[St. Peter] was part of the reason that council was called
No kidding. He had the vision of all foods becoming clean and he converted the first Gentile, so yes, definitely. He also did most of the speaking.
he was pope before he had the Holy Spirit
Or, at least, he received the command to become one. Protestant translations, by the way, routinely insert "elder" where either "episcopos" (bishop) or "presbyteros" (priest) is used in the original. This is just not a belief system based on honesty. Anyway, if you tell me which verse in your translation identified Peter as "elder" I will tell you what the Bible really says.