Shoulder clunking, easy fix on the left?, harder on the right...

[neurospast]

Both your shoulders have the same problem, well I think, but at a different stage. Your right is the worsed of the 2 but don't be surpriced if left will catch up with right! What I read is that you are doing a lot of work in the gym. Personally I think gym work has a tendency to cause problems: 1 majority of exercise are focused on the front (mirror side of body) Big pecs, huge upper traps, even bigger Latissimus Dorsi. What the mirror doesn't show is the back where all the compensation can be seen for all the easy muscle pumping exercises which have enhanced the front. 2) every one goes to the gym, hardly anyone has a clue what they are doing, tendency to push more weight then reasonable (well gyms and competition goes together I suppose).
My point is that most likely you have created a disbalance between internal and external rotators, having a poor control of your scapula movements and none excisting Rotatorcuff function. All control being destroyed by the power muscles taking over functions regarding Scapula and Gleno-Humeral control and strength. Just to give you an example your clicking on the left is likely caused by tight internal rotators (check length of Pectoralis Major, Minor and Latissimus Dorsi (how to do you'll find likely on the net) Check weakness of external rotators.
By the way when you move your arms above your head with elbows straight, do you have to move on some directions your head forwards? Are you able to look at the ceiling or do you get some pain at your neck when doing it?
To be honoust you need to see a Sports- physiotherapist or a good sports therapist to get advice on these problems. That you had an MRI of your right shoulder? should give you a hint of how severe these problems might be (maybe not today but next year or the year after)
Hope to have scared you enough, good luck. I do not think it would be a good advice to give you exercises as so because shoulder problems tend to be more complicated and can respond very badly with the wrong advice on exercise.