Sorry to take a while to answer. Someone else got to your question before me, and that moved you off the top of the line.
Frequently, I see arthritis of the AC joint in weight lifters. Usually, this injury is aggravated by bench work (particularly inclines) and push ups. It will awaken you from sleep if you lie on it, and can cause popping and grinding in the shoulder with activity. You didnt mention it, but typically, AC problems will cause pain when you are reaching across your body with the effected arm, such as when you put on deoderant.
The injury can usually be detected on a plain Xray, and quite easily on MRI. That part of your story is confusing. However assuming the studies gave false negatives, it is possible to make the diagnosis by injecting lidocaine in the AC joint and seeing if the symptoms are temporarily relieved.
If AC arthritis is present, and all else has failed, surgery can be done arthroscopically, and has a very high rate of success.
The full repair of your tendon my not have occurred due to poor circulation. Getting alternative hot and cold to the area will stimulate the blood flow.