There are many evidences within his own writings that his thorn in his flesh was his eyesight.
He was roundly abused and stoned a number of times, even left for dead once.
His ending of the letter to the Galatians, I believe, is "see what large letters I use." Assuming that the large letters were necessary because he couldn't see small ones, and assuming that the stonings might have also hit his face and injured his eyes, then the "flesh" that needed repair would have been eyes.
I always figured that Paul's "large letters" language referred to the fact that he was illiterate. The fact that what he was saying was being scripted by a scribe and then he'd, so the churches he was writing to would know it was him, would script a couple of lines in his own hand.
Just what I was taught in my Christianity classes...