Okay, so the first diagnosis was correct. I believe it started with the ac joint.
I think I suffered a separation due to repetitive movements under load (can shoulder separation happen because of repetitive stress or does it always happen due to macrotrauma?). Perhaps I also sprained some ligaments in the back area (upper traps I think) while military pressing (I did have a crick in the neck after one session I remember).
I went to not one but 3-4 orthopedic surgeons. I had anMRI/MRA done. MRI/MRA both indicated no tear in labrum but thickening of posterior supraspinatus tendon. I educated myself on the shoulder anatomy during these two years since I noticed the clicking. Interestingly, both MRI and MRA reports said that I had a normal AC joint.
However, I recently (in March 2010) had an xray taken. Attached is the xray image. I think It clearly shows separated shoulder (does it?). The ortho I showed it to just shrugged it off without even looking at it properly. He said I would be fine by strengthening the RC.
Here is my own take on the whole thing:
I have looked at quite a few xrays during my own research and I think the clavicle's distal end should be flat, not pointed. The pointed end (osteophyte) shows bone growth there which perhaps happened as a result of microtrauma? (I don't remember ac joint pain anytime in the past year). Or perhaps the growth happened with the clicking/rubbing after the separation.
In either case, I think first the separation happened, then because the scapula lowered down, the subacromial space decreased. And due to my overhead activities I developed tendonosis of the supraspinatus. I think the tendonosis of the supraspinatus is a symptom, not the main issue. The main issue is the drooping of the scapula. Note that there is an external step deformity that none of the orthos I went to bothered to examine (since I didn't report any AC pain).
How to cure it? I don't know. I need to somehow raise the scapula back in line with the clavicle. In doing so, I think the subacromial space will increase and impingment will not happen anymore. I really want to return to going back to the gym and doing heavy upperbody work which I have not done since 8 months into the clicking.
Personally I also think orthos didn't guide me properly and didn't even bother to notice this separation until 2 months after the clicking. Perhaps a screw would have prevented this situation.
That's my own theory (ortho still thinks I need to keep doing PT on therotator cuff that I have been doing for the past 2 years). Does someone have differing opinions?
I am pretty sick of the shoulder being the way it is (pain when doing overhead activities deep within the shoulder, lots of instability, clicking, popping, etc. ) and want a normal shoulder now!