I too lost a LOT of weight and just about all my muscle before my surgery in 1984. And Yes, it was a long recuperation time for me with a lot of the pain in my back. It will get better. Your muscles just need to be strengthened and retrained. Hang in there. I know it is painful. I sure hope therapy works for you. I really believe that the more ill you are going into this surgery, the longer the recovery time. It's not just incisions that have to recover, but the whole body. I think you are experiencing that. Are you getting plenty of magnesium and potassium? Maybe some of the discomfort is related to cramping of the muscles that come with working them more than they are accustomed to? Just a thought worth asking your PT person.
I'll be thinking of you and wish you the best.
Diagnosed with CD in 1979, many resections and meds
Perm Ileostomy July 1984 at Cleveland Clinic
Disease free since surgery