Your citations from II Peter carry no weight, for the book is a forgery.
(1) Six documents which, by tradition, are bound into the English Bible have no rightful place in the Canon of Scripture. The command "Prove all things" (I Thessalonians 5:21) has to do with canonicity; it is a command which is to be obeyed by each Christian.
However, Protestants, having been taught that questions regarding canonicity were settled by so-called "Church Councils" convened several times over the first several centuries of the present Age of the Reign of the Christ, have abnegated this vital responsibility.
Historical accounts of those "councils", together with the pronouncements made by those councils, reveal in them the working of the Mystery of Iniquity, of which the Apostle Paul warned (II Thessalonians 2:1-12).
(2) The church structure erected by the Apostles was that of a autonomous Local Assembly, governed by a Shepherd (termed "Pastor" in the Old English of the King James Version) who answered directly and exclusively to the Great Shepherd, the Lord, Christ Jesus. The Shepherd (POIMEN), having several functions, has several titles; the titles include PRESBUTEROS ("Elder"), EPISKOPOS ("Overseer"), and DIDASKALOS ("Teacher"). Moreover, the Shepherd has received directly from the Lord Christ the spiritual gift POIMEN KAI DIDASKALOS ("Shepherd, even Teacher"), Ephesians 4:11.
Within the assembly, a number of individuals have the function of deacon (DIAKONOS, "Servant" or "Administrator"). Protestants generally construe the Shepherd to be answerable to the assemblage of Deacons; but that is a grave error and a perversion of the divinely-instituted order.
(3) Virtually nothing is known regarding the activity of Local Assemblies during the historical era which began upon the death of the last Apostle (who almost certainly was not John) and lasted about a hundred years. However, historians note that the Church emerging from that century of obscurity is not the Church of the Apostolic Era, being radically different in structure. The "flat" structure of the Apostolic Church has vanished, being supplanted by a hierarchical structure in which the Shepherd of the Local Assembly reports to a supervisor who oversees a number of Local Assemblies, and so forth, the structure having several tiers. The hierarchical Church today is known as the Papacy, the Church of Rome.
(4) Paul tells the Thessalonians that the Mystery of Iniquity already was at work, II Thessalonians 2:7. Moreover, Paul notes that he (Paul) alone restrained operation of the Mystery, II Thessalonians 2:6-8. Not until the restraint, Paul, was taken out of the way by death, would the Mystery be able to come into full bloom, installing at the head of the tiered structure the Man of Sin, the Pope.
The working of the Mystery is seen in the council of the Apostles in Jerusalem, Acts 21:17-26. From this account of the council, together with other passages of the Scripture, it is evident that James of Jerusalem, who is not one of the Twelve, is a false apostle and the primary subvertor of the Church. Moreover, it is apparent James of Jerusalem is the prototype of the Pope, for he presumes to give commands to the Twelve.
Subsequently, James is dispatches his zealot thugs to intimidate not only the Local Assemblies but also the Twelve, and James repeatedly commissions his zealot thugs in attempts to murder Paul. It is James of Jerusalem (and not a disease) who is the "Thorn in the Flesh" which so troubles the Apostle Paul.
(5) The Historian has in view the "Visible Church". But the Visible Church is not necessarily the Church of Christ Jesus. One researcher, E. H. Broadbent, published a book titled "The Pilgrim Church", in which he presents a convincing argument that, due to persecution by the Visible Church and its ally, the State, the true Church of Jesus was forced to go "underground".
[continued in next post...]