If I had to come up with a first draft of mechanics for Protein and Vitamin hidden stats, I’d say give them minimum values of 0 and maximum values of 1000 and let the Blood Analysis bionic reveal the exact value. Every 7 minutes (70 turns) they decrease by 1. If we have the player lose 1 Hunger whenever Protein is decremented, then shifting some of meat’s Calorie value toward Protein would automatically give us something akin to http://en.wikipedia.org/wiki/Rabbit_starvation.
As Health works now, it tends towards an equilibrium point of 0. Maybe change that to be -10+Protein/100+Vitamin/100.
I feel like having 500-1000 Protein should give bonuses of 0-10 Speed and 0-2 Strength, and 499-0 Protein should give penalties of 1-20 Speed, 1-5 Str, 1-2 Dex, 1-3 Int and 1-2 Per.
500-1000 Vitamin would be +0-2 Dex, Int, and Per. 499-0 Vitamin would be -1-3 Dex, -1-2 Int, and -1-3 Per.
One important thing to keep in mind when balancing the values on different foods is keeping the ratios on most foods such that you need to eat more than survival amounts to be healthy. Less than 5 Prot/Vit per 7 Cal, probably about a 1:2 ratio on most food that isn’t supposed to be excessively nutritious.
The Vitamins item is probably worth 50 points of Vitamin, and might need to be renamed Multi-Vitamins. A Chemistry Set recipe for Multi-Vitamins wouldn’t be too out of place, and a new Protein Bar item using Protein Powder would be a good addition.