It sounds very much like what I experienced, not enough for general MDs to give a clear cut dx of TOS , but definitely related to a long term chronic RSI w/ neck & upperback involvement.

I was 15 yrs @ assembly work, it took me 2.5 to get back to 75% - I did have to deal with work comp delays , or I probably would have found better help sooner.
Actually a very good chiropractor I found 1.5 yrs into it was my best help, then a PT teacher was very helpful by doing the top rib mobilization for me..
I was off work most of that time. or on very modified use..
IMO trying to work a demanding job and trying to recover does not work out well, what is most important , your health or the job?

I suggest finding some highly skilled PT /DC and learning as much as you can about body/posture/myofascial pain syndrome.

I think if you can address all those and stay with it you will see improvements long term..

I still use my far infrared heating pad often & my IF stim for flares as needed, often it is a long term thing to continue with even after the worse is resolved..

some things to do at home & other info-
http://neurotalk.psychcentral.com/album.php?albumid=422

How knowledgeable does the PT person seem to be?
Triggerpoint info - if you have TrPs they must be resolved first - before any stretching /strengthening will really help.
http://neurotalk.psychcentral.com/thread125577.html

useful sticky - post # 1 is a crash course of info links
http://neurotalk.psychcentral.com/thread84.html