When he shows up in the cowboy hat in The Impossible Astronaut at the start of the season, he says that he's 1103 years old. The Doctor who left Amy and Rory behind was 909 years old. So unless he was lying about his age at the start of the season (which is entirely possible), he spent nearly 200 years doing stuff after leaving Amy and Rory, and before saying goodbye to Craig and then going to meet his death. He suggested in the episode that he's been going around saying goodbye to people and wrapping up loose ends. Considering how much he gets into just on a yearly basis, it seems like he could have wrapped things up in less than 200 years. But there's also an indication that he's simply been knocking about doing little things and staying out of trouble for 200 years because he was trying to avoid his death. As he says in the opening of the season, "I've been running. It's time to stop."

That leaves the question of why he didn't appear to age if he's been running about for 200 years. Either the writers just didn't think to make him look older, or the Doctor was lying about his age for some reason, or it was the ganger Doctor because it's possible that the Flesh doesn't age.