Basicly I want there to be a chance of contracting diseases like Rockjoint from eating raw food, I've played around with it a bit, on a food items settings you can choose stuff like damage health, damage stamina etc... but not diseases.

You would probably have to script each item of food you wanted this to apply to. Unless you could somehow determine things on the player's end? Perhaps clever use of http://www.creationkit.com/HasMagicEffectWithKeyword_-_Actor or http://www.creationkit.com/HasEffectKeyword_-_ObjectReference because all food items bestow some sort of effect....