Summary: Points out clues from the scripture that point directly to the identity of the thorn in Paul's side
Paul’s Thorn in the Flesh
There has been much speculation over the centuries about just what Paul meant by his thorn in the flesh. Many have said it was some kind of sin which he just could not get behind him and others have said his thorn in the flesh was the persecution that followed him no matter where he went. I believe that his thorn in the flesh was indeed a physical malady that was a constant companion with him at all times.
It is important from the beginning that we see that Paul was highly educated because it will support what I have to say later. So let us briefly entertain the following scriptures.
Acts 22:2b Then Paul said:  "I am a Jew, born in Tarsus of Cilicia, but brought up in this city. Under Gamaliel I was thoroughly trained in the law of our fathers and was just as zealous for God as any of you are today.
AC 26:4 "The Jews all know the way I have lived ever since I was a child, from the beginning of my life in my own country, and also in Jerusalem.  They have known me for a long time and can testify, if they are willing, that according to the strictest sect of our religion, I lived as a Pharisee.
Philippians 3:4b If anyone else thinks he has reasons to put confidence in the flesh, I have more:  circumcised on the eighth day, of the people of Israel, of the tribe of Benjamin, a Hebrew of Hebrews; in regard to the law, a Pharisee;  as for zeal, persecuting the church; as for legalistic righteousness, faultless.
The above scriptures are presented in order for us to see that Paul was a highly educated person. He was trained from childhood under Gamaliel who was one of the most recognized teachers of Judaism of his time. The scriptures tell us he was fluent in Hebrew, Aramaic and likely Greek. His education for his day and time was far above average as was his training on the Jewish Law (The first five books of our bible). In short Paul was very intelligent probably higher than our PhD’s of today. He spoke read and wrote in Hebrew and Aramaic and likely Greek. His knowledge of God from the Jewish standpoint was just about flawless. We would consider him brilliant today.
Now that we see that Paul was highly educated for his time and well recognized as a vibrant Pharisee among Pharisees let us continue looking at his thorn in the side.
Paul introduces his thorn in the side in the following verses. In previous verses he had been speaking of visions that he had been given from the Lord and he continues with the following statement.
2CO 12:7 To keep me from becoming conceited because of these surpassingly great revelations, there was given me a thorn in my flesh, a messenger of Satan, to torment me.  Three times I pleaded with the Lord to take it away from me.  But he said to me, "My grace is sufficient for you, for my power is made perfect in weakness." Therefore I will boast all the more gladly about my weaknesses, so that Christ's power may rest on me.  That is why, for Christ's sake, I delight in weaknesses, in insults, in hardships, in persecutions, in difficulties. For when I am weak, then I am strong.
We can see here that Paul talked about a thorn in his flesh that tormented him and that its intent was to keep him humble. We also note that it was significant enough that it interfered with his daily life. So much so that he pleaded with the Lord three times to take it away from him. But the Lord did not answer his request saying instead that His grace was sufficient for Paul for the Lord’s power is made perfect in human weakness.
It is well known that the Pharisee Saul (Paul) was a major persecutor of the early church (called The Way). He was so intent on wiping out what he considered this major affront to Judaism that he even got letters from the high priest that allowed him to go into different nations to find Christians and bring them back to Jerusalem for trial. Most of us are familiar with his meeting the Lord on the road to Damascus to capture Christians. I include that part of scripture here because of its importance
AC 9:1 Meanwhile, Saul was still breathing out murderous threats against the Lord's disciples. He went to the high priest  and asked him for letters to the synagogues in Damascus, so that if he found any there who belonged to the Way, whether men or women, he might take them as prisoners to Jerusalem.  As he neared Damascus on his journey, suddenly a light from heaven flashed around him.  He fell to the ground and heard a voice say to him, "Saul, Saul, why do you persecute me?"