What Causes Pain In Shoulder And Difficulty In Breathing?

My 53 year old brother had an appendectomy on February 1, 2015. He had abdominal pain from the time he came home. He could not eat and has lost almost 40 lbs. He needed to lose it but not like that. On March 3 he developed pain up the right side and shoulder and started having trouble breathing. He was sent for gall bladder testing by his pcp. The hospital who did the testing said tests were negative and sent him home. Within 2 hours he went to a different hospital and was admitted with severe pneumonia. He still has severe side and abdominal pain though and the hospital cannot figure out why he has this pain. He cannot come home until they figure out what is wrong. He is on IV antibiotics for pneumonia. It also hurts for him to breathe but the pain is not all from the lungs he is sure. He has never been ill in his life. He had lower back surgery 3 years ago and had a piece of his thyroid removed 2 years ago but has been fine since then. He takes thyroid medicine and HBP medicine but nothing else. His heart is fine and his cholesterol is fine. Any idea what could be wrong with him?