Hmmm, its a weird one, maybe it is as you said, an emphasis on upper body work. Maybe you need to do some stretches before you start your workout, do you have a good warm up before lifting and a light stretch? it may help if you don't already do it.
Also, do you pyramid up in weights before you do your work sets? I do this now as before I was going straight to work sets after my initial warm up and done an injury in my lower back.
Is their a reason your avoiding the above squats/deads/rows?
I can't squat at the moment because I've fuuurked my knee, but I can still dead and row. I would suggest you put them back in your routine if you are not injured as they are the mass builders, especially squats and deads.
Hope you work it out mate, friggen sux arse having an basted injury or niggly proplem.