Hey Tottie,

Firstly the shoulder is complex - lots of structure are involved.
Cracking of the shoulder isn't a problem unless it hurts really. You could have hurt yourself in lots of ways 5 years ago but by now most of them should have healed. It's quite possible that pain with internal rotation is a result of lack of motion of the shoulder when you were injured. Now when you internally rotate you are trying to go into a range that you have lost and is thus quite painful. Stretching would help this.
However, there are some structures that if injured will take a very long time to heal and possibly not heal without surgery (you would have to decide how much this problem bothers you). An example of this is a torn labrum. For you to know you would need a scan of the shoulder.

My advise to you is to visit a physio and get a thorough assessment there are too many things that could be giving you pain and I'd be unable to tell you without seeing the shoulder.

Cheers,
Puddin