If you have pinpointed the cause of your discomfort as your computer use, then you need to change the way you are working on the computer.
Back in the old days, before the widespread use of computers, people using typewriters did a lot more different types of activities during the day, and got up and moved around more. Back then, they would stretch reaching down to get some paper for the typewriter, then reach up to put it in. During typing they had to reach up and move the carriage back at the end of each sentence. If a mistake was made, they leaned forward to correct the mistake, using both upper extremities. When the document was done, they got up, walked to the filing cabinet or mail room, to have the document filed or sent on its way.
Now days, about the only part of the body that workers use is the fingers. They sit statically at the keyboard, rarely moving or stretching. When the document is done, they just hit the enter key and start on the next.
If the person stops every so often and stretches, it can alleviate a lot of the "over use" and "repetitive syndrome" conditions.
You do not have to get up, but stretching the hands and shoulders, rotating the neck every 10 minutes or so will go a long way. At the end of each document, get up and move a little. Bend down or squat a couple of times, stretch the lower and upper back, you do not have to leave your area to do 30 seconds to a minute of stretching. Do this at least once an hour. When you do get a break, do walk somewhere, even if it is down the hall a couple of times.
Also, make sure that your workstation is ergonomically built for you. Your forearms should be supported and your wrists should be in neutral when you type. The monitor should be such that you do not have to strain to see it. Your chair should be at a height that your feet on flat on the floor and your back supported.
Most businesses can have a workstation evaluated to make sure it is proper, if you ask.
But, again, it is up to you to stretch and move around, do not just sit there getting stiff and sore.
And since we are so sedentary in our work now days, it is important to work on cardiac endurance (aerobic capacity) and strength when we are at home. Walking is a very good exercise for over all fitness, but biking and swimming are also good. Yoga, tai chi help with range of motion of all of the joints and balance. If you prefer, athletics and sports also are good for strengthening and endurance. The point being, just get out and do something.
We have to keep ourselves in good physical condition. Physicians cannot do much for the overuse and repetitive stress problems associated with our work. It is not really up to them to treat the everyday aches and pain of everyday life. That's up to us, to care for our own bodies.
This may be rather late as a reply but have you read up on Palindromic Arthritis? I was diagnosed with Rheumatoid Arthritis but did not fitost of the profile for it. Eventually diagnosed as Pallindromic which travels and mine always starts in my shoulders and goes from one to the other. You do speak of a flare which is what you get with arthritis although you dont mention other parts of your body. My first flare was bad and I also had it in my legs (couldn't walk) and eventually left my shoulders (couldn't raise my arms) and had it bad in my wrists and fingers. Was quickly referred to Rheumatologist who started me on treatment and it gradually went. Was on meds for a few years with no episodes so took myself off. Stayed clear for 10 months and then it flared again starting in my shoulders. I was still under rhuematologist so he quickly got me some steroids which eased it and now I am on meds again which I guess I will have to be sensible about and keep taking.
May be worth you looking into this as it could be wehat you have but you only get in your shoulders. Jan