Generally if you have trigger points , stretching isn't going to do you any good until those TrPs get resolved.
That's something Sharon Butler doesn't cover, trigger points.
..they are real and they happen!

Was the PT just rubbing on those muscles or actually doing manual TrP release?
*a specific pressure on 1 TrP at a time until it fades away.*
TrP sticky thread-
http://neurotalk.psychcentral.com/thread125577.html

If your muscles are in spasms also then that needs to be addressed -
I had best luck with my chiro doing the ultrasound, low level laser, IF stim (low setting only - like a soft massaging - nothing that tightens the muscles)
but mine were not as hyper sensitive as yours sound like..

I saw a website that tells about a way to work trigger points w/ ultrasound I'll see if I can locate that.
LLLT (low level laser therapy) may work in the same way without having actual pressure of touching..


Found it- explore the whole site and the practitioner topics , maybe share it w/ PT person to see what they think about it.
you could also have a co condition of fibromyalgia... others have developed it along w/ TOS.
http://www.drlowe.com/myofascial/pra...ltrasound1.htm