Ok, first off visit the doctor.
Then take a long look at your work place. Is it set up properly? When sitting in your chair with your feet flat on your ground your knees should be at almost exactly 90 degrees angle. Preferably your chair has lumbar support so you don't stress your spine. (Also, you do remove your wallet from your back pocket before sitting for six hours I hope?)
Your upper arm should be vertical, with a 90 degree bend at the elbow, and you should grip the mouse
in front of your chest. You primarily use the mouse when playing, and the primary tool should be in front of the chest. The reason it's 'usually' off to the side is because people use the keyboard and only occasionally the mouse. Not so in our profession.
Get a mouse for your non-dominant hand, and use it 75% of the time for a few months. Go to a good store and try out other pointing devices. A trackball for variation does wonders. Get a vertical mouse, like the ones from
Evoluent.
To understand why you want this just hold out your hand like you'd shake someone's hand. Place the pinky side of your hand on the work table. Slowly twist your hand inward until the palm is on the table and feel what happens in your joints, the bones of the lower arm and your shoulder. Then go buy a vertical mouse.
Take micro pauses in work, stretch, lean your head, roll your shoulders. Do this every single time there is a two second lull in the action, and when you are pondering a decision.
Once the shoulder stops hurting start going to the gym four days a week. There is
no getting away from this one unless you want to be a cripple in a few years time. Get a professional trainer to help you learn the ropes and design a program for a three month period. Revisit him after that time for a new program and follow ups.