Sounds really bad.
I'd be stopping the PT until it is sorted, as you may be aggravating an injured muscle, tendon etc.
Exercise must be specifically tailored to your condition.
I had to modify mine as a few made me worse.
With all of that trauma to your body, add into the equation muscle knots, tension, soreness etc. You are bound to have all sorts of sore and suffering muscles as your body tries to keep going, and also protect itself. This will cause a lot of pain.
Doctors tend to ignore this aspect, but you will need remedial massage as part of your treatment and recovery.
I was amazed at how much my pain levels dropped with this treatment.
Hasn't cured me, but have had a BIG improvement in pain levels.