Catholics have always recognized James as Bishop of Jerusalem. That’s exactly what I described: Peter sets the doctrine, and James implements it in his see.
As for you citations, you really should read something in its original context before you cite it. Your citation of Clement of Alexandria confuses the actual writings of Clement with another author’s citation of it. Clement of Alexandria actually cites Clement of Rome’s first epistle as “aposotolic,” even as if it were scripture itself. (The New Testament was still in a bit of a state of flux when Clement of Alexandria wrote.) In this first epistle, Clement of Rome affirms primacy over other sees. Now, our Eastern brethren disagree with the Catholic assertion that Clement of Rome’s primacy amounted to the authority of the papacy, but it certainly establishes that Peter’s see, not James’ see, was that of the primate.
In fact, time and time again throughout the New Testament, Peter is called “primus,” (first) when he was, in fact, *not* the first of the apostles. He *was* the first to witness the resurrected Christ, but only because John stopped and allowed him to enter first, a clear deference. And there are so many times when the other disciples ask Peter to ask Jesus something.
You might want to check your facts on Peter being the first to witness the resurrected Christ. Luke notes women were the first to enter the tomb.
Your assertion that John stopped to let Peter go in first is just that....an assertion with no proof. Recall, John outran Peter to the tomb. John got there first and saw the empty tomb but did not go into the tomb. Peter went on in to the tomb. One can understand why after his actions in denying Christ as he did.