Sorry to hear that I'm definitely not an expert, but is it possible he had mites? They can transfer some nasty stuff. It sounds like you've been worrying about it being contagious, and I don't want to stress you out further but I did have a sorta-similar situation happen to me about a year ago. I had a baby die after a couple of weeks from a disease. She did hold her head at a funny angle, and then it affected almost her entire body before she died half a day later.

Hopefully (as bad as that sounds) it was just a birth defect or something vs it being contagious. Good luck.