Great post by Adam, I had the same type of injuries years ago and went to hospital and got a cortisone shot in the shoulder right in the AC joint. I had a real bad imbalance between my front delts/pecs and rear delts which has caused some problems over the years until I put the effort in for the small muscles and got away from the showy muscle work !!.

Another point worth noting is that if you are also doing weights the problem can come from bicep work as the tendon runs up through the front of the shoulder at the AC joint. That was partly my problem through bad form when lifting.

A good physio can give you some great stuff to work on which you can even do sitting at a desk which is great for anyone stuck in an office.