Don't be afraid to adjust the reps your PT gave you based on feelings and symptoms. Sometimes they don't realize we have to go easier.

The shrugs are consistent with that study I linked to.

Also, I have your same problem of collar bones that are too flat. Originally my left one, which is my TOS side, was even slightly pointed down.

For me, wall pushups were an awful experience. As I built up muscle and tightness in the upper chest, the compression increased. Wall pushups are now on my personal "DO NOT DO" list.

Another bad move for me is sitting in a chair with my hips forward and my trunk leaned back such that my upper back is pressed into the back of the chair. Too much of that and I can flare up.

I get a lot of muscle tightness too. Stretching helps, but I haven't been told not to stretch. If you want a really small and effective stretch set to try, I recommend the book "3 Minutes..." by Weisberg. The title is overhyped, but still a great book.

Other tightness helps are supplementing with magnesium (search the forums) and some kind of muscle relaxant. Diazepam can be used for that purpose and some of us take it 2mg 2 X per day.

I've also gotten decreases in muscle tone by listening to relaxation audios. I really like Infinite Relaxation for the iPhone/iPad.

HTH. Good luck.