It sounds like you have a tendon injury around the AC joint and it's badly inflamed, causing pain during lifts.
If I were you I'd get it looked at by a professional before continuing lifting, otherwise you run the risk of either making the injury worse, or preventing the existing injury from healing.
Without knowing how serious it is, noone can really tell you how to adjust your programming. The Jefferson squat (I have no idea what that is btw) may not cause pain, but that doesn't necessarily mean it's safe for your injured shoulder.
I've got rotator cuff issues but have never encountered pain while deadlifting. In fact it's the one lift I know I can always do, regardless of my shoulder status haha. Good luck.