Smoke, after James is killed in chapter twelve, who is the James that is referred to in the remaining chapters?
I think it's obviously Jesus' brother James. James the son of Zebedee was already dead.
You've misunderstood the timeline. Acts doesn't precisely agree with Galatians, but I think we can piece a better timeline together.
Acts says that after his visionary experience Paul continued on to Damascus, then "after many days" he went to Jerusalem, where "he assayed to join himself to the disciples: but they were all afraid of him, and believed not that he was a disciple. But Barnabas took him, and brought him to the apostles, and declared unto them how he had seen the Lord in the way, and that he had spoken to him, and how he had preached boldly at Damascus in the name of Jesus. And he was with them coming in and going out at Jerusalem."
Paul says: "Neither went I up to Jerusalem to them which were apostles before me; but I went into Arabia, and returned again unto Damascus. Then after three years I went up to Jerusalem to see Peter, and abode with him fifteen days. But other of the apostles saw I none, save James the Lord's brother."
Despite the obvious difficulty here -- Acts makes it sound like Paul was much better acquainted with the community than Paul's account does -- I think this is the same visit.
"Afterwards," Paul says, "I came into the regions of Syria and Cilicia." Acts says, "And he spake boldly in the name of the Lord Jesus, and disputed against the Grecians: but they went about to slay him. Which when the brethren knew, they brought him down to Caesarea, and sent him forth to Tarsus."
Tarsus was in Cilicia, so both accounts show him going to Cilicia after this visit.
Then, in Acts 11, Barnabas goes to Tarsus to get Saul, and brings him back to Antioch. A prophet from Jerusalem comes to Antioch and predicts a great famine, so the folks at Antioch take up a collection and send it to Jerusalem by Barnabas and Saul.
While Saul is at Jerusalem, James the son of Zebedee gets killed (at the beginning of chapter 12), and only after that (at the end of chapter 12) do Saul and Barnabas return to Antioch. The Antiochians send them off on what is traditionally called Paul's first missionary journey, which is described in chapters 13 and 14.
Then a theological disagreement comes up, and Paul goes to Jerusalem to defend his position.
Acts describes it like this:
And certain men which came down from Judaea 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 other of them, should go up to Jerusalem unto the apostles and elders about this question.
And being brought on their way by the church, they passed through Phenice and Samaria, declaring the conversion of the Gentiles: and they caused great joy unto all the brethren.
And when they were come to Jerusalem, they were received of the church, and of the apostles and elders, and they declared all things that God had done with them.
But there rose up certain of the sect of the Pharisees which believed, saying, That it was needful to circumcise them, and to command them to keep the law of Moses.
And the apostles and elders came together for to consider of this matter.
Paul describes it like this:
Then fourteen years after I went up again to Jerusalem with Barnabas, and took Titus with me also.
And I went up by revelation, and communicated unto them that gospel which I preach among the Gentiles, but privately to them which were of reputation, lest by any means I should run, or had run, in vain.
But neither Titus, who was with me, being a Greek, was compelled to be circumcised:
And that because of false brethren unawares brought in, who came in privily to spy out our liberty which we have in Christ Jesus, that they might bring us into bondage:
To whom we gave place by subjection, no, not for an hour; that the truth of the gospel might continue with you.
Paul's account is more strident, but the point is that this is the same visit. Paul, when he speaks of meeting "James, Cephas, and John, who seemed to be pillars," is clearly talking about this meeting at Jerusalem, which was presided over by James.
James the son of Zebedee was already dead. James the brother of Jesus, "who seemed to be [a pillar]," is the one who presided over that council and the one who rendered a decision at it. The whole circumcision controversy was after the death of James the son of Zebedee.
