There are systemic infections and viruses that do not go away. Be persistent in looking for an answer. Get to different doctors. I'd see a naturopath.
Better go see the quack. Maybe its a pinched nerve, those can stir up a shitstorm which can be never ending. But whatever, sounds too serious to be looking for an answer here. Better go see that quack and INSIST he look at everything.
i don't know but i saw on the discovery health channel on "mystery diagnosis" there was a guy who ate some sort of chicken and there was a parasite or something in the chicken that began to destroy his nerves and muscles. not sure if this is related but you had better notify a medical professional ASAP.
Time for a trip to the doctor....A virus can last 3 weeks....but the shooting pains in the chest and underarms...and his sensitivity to you touching him, is very concerning.....Good luck.