My Son Has Always Been Athletic - Played Year Round

My son has always been athletic - played year round sports. Ending up having shoulder surgery 3 times in the last 3 yrs. Hes in PT now and won't be cleared for sports until October but he isn't planning on it anyways. He was running as soon as the orthopedic gave him clearance to start running. that was going good but he stopped running about 2 weeks ago saying he was uncomfortable. He has always had cracking knees but now he is starting to be super stiff in the mornings and when he stands up and pushes himself off the bed you hear his elbow crack, then as he stands his knees and then as he walks his hips and ankles. hes only 16 and my son says it feels like hes 100 years old. what is going on?