Jake, A common error in getting that elbow turned is to do it by rolling the shoulder forward to cause the elbow to rotate.
Try this: stand near a corner of a wall and place your bow hand on the corner (like holding the bow). Now practice turning the elbow WITHOUT ANY shoulder movement. You CAN learn this, it just takes a little practice -- keep your shoulder down and back and just turn your arm. Once you learn this movement, you will be able to do it with the hand unsupported by the wall. It sounds like the discomfort you are experiencing is a result of getting the shoulder out of position.
Arne