Yogurt's not so bad because the microbes make it more "alive" and with more enzymes. Cultured things aren't totally dead. :)
So did you have actual growths or spurs freezing your shoulder joint? I think my brother had something come up on the x-ray. Altho I wouldn't be surprised if he had parasites, he's always out climbing mountains and eating just about anything anywhere!
make sure, as you adjust your diet, that it includes plenty of good oils like flax and calcium sources.