This AfterEffects script sorts layers in a composition according to their in-points.

sortlayers.jsx

/*
 * This AfterEffects script sorts layers in a composition according to their in-points.
 * 
 * 1. Save this file as "sortlayers.jsx".
 * 2. Select a target composition in project panel of your AfterEffects.
 * 3. Run "sortlayers.jsx" from Menu->"File"->"Scripts"->"Run Script File".
 */
app.beginUndoGroup("Sort layers");
var item = app.project.activeItem;
if (item != null && item instanceof CompItem) {
  for (var i = 1; i <= item.layers.length; ++i) {
    var cur = i;
    while (true) {
      if (cur-1 > 0 && item.layers[cur].inPoint > item.layers[cur-1].inPoint) {
        item.layers[cur].moveBefore(item.layers[cur-1]);
        --cur;
      }
      else {
        break;
      }
    }
  }
}
else {
  alert("Choose a target comp in project panel.");
}