I started Wendler's 5/3/1 yesterday... had a good workout, I started the program with with Overhead Press. Was planning on going Press, Dead, Bench, Squat for a 4 day split, in that order. Now my problem is that I've had several shoulder injuries due to a lot of martial arts training and lifting in the past... specifically around the AC joint. When I did a normal deadlift, I felt an extreme pain in my left shoulder. Next week I was gonna try to swap my deadlift and squat days to see if it's just soreness/hurting because I did overhead presses yesterday. However, after failing with the Deadlifts, I decided to try a set of Jefferson Squats, and there was no pain. So I was wondering if the Jefferson Squats and Deadlift Mechanics were similar enough to just keep using the Jefferson Squats for the program if the pain doesn't go away in the shoulder. If not, what could I do to work around all this mess for now?

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.

I'd do some shoulder dislocations with a PVC pipe to see if that helps/hurts. Go look on YouTube for examples. They really helped my shoulders get healthy and mobile after I injured them doing farmers walks and heavy DB pressing. 3x12, three times a day. If that doesn't help, get a doctor.

Also, IMHO, the Jefferson squat doesn't look like it'd be a great max effort movement.