You're doing a lot of heavy work (deads, bench, squats etc) and you said the pain seems to be coming from under the bone. I would suggest that maybe you have rotator cuff weakness or a tear, or a tear waiting to happen. The supraspinatus muscle runs under the clavicle.
There are 4 ROTATOR CUFF MUSCLES: Subscapularis, Infraspinatus, Teres minor, Supraspinatus.
There are tests you can do to test the strength of your rotator cuff muscles. Visiting a good sport doctor would be a good idea to find out where your weakness is so you can take the appropriate corrective measures.
Whatever you do, DON'T try to work through the pain. A full tear will require surgery.