Add a List to you UserControl:
private List<PictureBox> Pictures = new List<PictureBox>();
Then when you add it to the controls list, you also add it to the Pictures:
PictureBox pb = new PictureBox();
pb.Location = new Point(oldPb.X, oldPb.Y + 100);
pb.Size = oldPb.Size;
Controls.Add(pb);
Pictures.Add(pb);
When you want to access it, you can do it by index, in the order you added them:
PictureBox toChange = Pictures[3];
(Obviously, you will want to make sure there are enough PictureBoxes in the list with the Count property before you try to get it!)