In the days of the early church, although there was one church for both Jew and Gentile, there were two heads of the church on earth. The Gentile churches taught by Paul, seemed to operate relatively independently of the Jewish churches taught by Peter and the others. Paul asserts this independence in Galatians 2:7-9: when they saw that the gospel of the uncircumcision was committed unto me, as the gospel of the circumcision was unto Peter (for he that wrought effectually in Peter to the apostleship of the circumcision, the same was mighty in me toward the Gentiles:) and when James, Cephas, and John, who seemed to be pillars, perceived the grace that was given unto me, they gave to me and Barnabas the right hands of fellowship; that we should go unto the heathen, and they unto the circumcision. So here we see two branches of the church even in its early days.
The reason Barnabas and Paul went to Jerusalem to find out about the question of the ceremonial law of Moses, was not because they did not know the answer, nor was it that they needed authority from the Jerusalem apostles. Rather it was to undermine the false Jerusalem authority claimed by some who taught the false doctrine reported in Acts 15:1,2: And certain men which came down from Judea taught the brethren, and said, Except ye be circumcised after the manner of Moses, ye cannot be saved. When therefore Paul and Barnabas had no small dissension and disputation with them, they determined that Paul and Barnabas, and certain others of them, should go up to Jerusalem unto the apostles and elders about the question.
The conference at Jerusalem affirmed Paul's doctrine. The effect of this was not to bring Paul's churches under Jerusalem authority but rather to affirm Paul's authority over the Gentile churches which he had established. Paul did not need to learn from the Jerusalem church and said: they who seemed to be somewhat in conference added nothing to me. (Galatians 2:6)
We should also remember that it is God's will that: there should be no schism (division) in the body. (1 Corinthians 12:25) We must remember that Jesus Christ in heaven is the ultimate head of the church, as far as organisation, although no one has a perfect understanding of His mind. We should look to our heavenly Father for understanding of doctrine.
The ceremonies of baptism and of laying on of hands should associate a person with the whole church. If you are in a schism they are invalid. Imperfection in the Roman Catholic church is no reason to leave it. The local pastor is only there to help you to be God's disciple. Remember the word that God spoke to Abraham: I am the Almighty God; walk before me, and be thou perfect. (Genesis 17:1) We should remember to walk before God, seeking first His approval, rather than man's.