Your situation is more common than you would think, so don't feel badly. First off, the MRI was negative, which is a huge plus.

Because scapular movement plays such a major role in shoulder movement, any muscle that moves the scapula can get affected, subsequently tighten/spasm and cause even more issues, including: pain in those muscles themselves, messing with smooth shoulder movement and causing impingement (rotator cuff and possibly long head of the biceps) and also radiating pain away from the muscles down into the shoulder and arm, mimicking a shoulder issue.

Then on top of that the cervical and thoracic spine start to get affected, start to tighten/spasm and they too can refer pain down into the shoulder and arm.

Bottom line, is that this a mess and confusing because you don't really know what the primary culprit is and just how much everything else is contributing.

However, like I said to start - your MRI was negative, so you rule out structure damage of the shoulder - that's GREAT news. So now talk to your therapist and see if they can broaden their approach to include the scapular region, thoracic and cervical spine. Hell, maybe even seek out a chiropractor to make adjustments. Plus I've seen many chiropractors offer deep tissue massage as well, because they go so well together.

Question: as an iron-worker, how often are you doing overhead work and in particular, is your head and neck extended, that is you are looking upwards? The reason I ask, is this is a VERY common issue for cervical issues.