Hey AJ,
I'm glad you are giving it a shot.
If he is in pain he will probably cry and lick or fuss with his paws over the area that hurts--for a sore head, he will rub it with his paws, for a sore belly he will lie curled up and lick himself or cry. To find out if your pup if suffering, find out how humans feel who have liver disease. Likely it is similar. But remember what I said about suffering--dog's don't "suffer" as much as we do because they have a sort of Buddhist-Zen attitude about the world and just accept everything that happens to them without getting all worked up about it. I feel strongly that they should be the ones to decide if their life is worth living--and I think they would almost always say "yes", as long as they are alive enough to feel the sun shine on their fur and know that you love them.
Quick word about diet--if you plan to feed the low-toxicity diet for a long time (either because you are saving up for the surgery or because you are hoping surgery won't be needed) you should be very careful about your puppy's nutritive needs. Low-protein diets might be tough for the pup to grow to full size and health at such a young age.
You might try replacing one meal a day with the homemade food, and either just barely cook the meat (make sure it's still VERY rare) or add a raw egg (you can get salmonella-free eggs from the Country Hen, they have a website so you can find a dealer). That would be easier than home-cooking ALL their meals, and also help make sure they can get all their vital amino acids, since raw or minimally-cooked proteins are more complete.
I noticed that egg is the protein used by your science diet kibble so maybe that would be the best choice if you can manage it. I also noticed that they are adding extra antioxidants, so I would recommend giving the puppy the occasional cherry tomato or piece of bell pepper if he will eat them--this is because the antioxidants in kibble and canned food are often lost or reduced in processing. Tomatoes and bell peppers are better sources of antioxidants than oranges and most dogs (that I have met) don't like oranges anyway. You can cook the bell peppers if he likes them better that way but the tomatoes should be raw. I get my dog to eat them by putting a little bit of lowfat mayonnaise on them, or you could try fat-free cream cheese (I think fat intake is supposed to be regulated, that's why fat-free).
Honestly I think kibble is just fine for dogs as long as it is supplemented effectively with fresh foods. For a normal dog you could just agg eggs and meat to the kibble without cooking anything special, but for your pup that would result in too much protein, so you would need to balance it with whatever starch your home recipe calls for, plus vitamins for nutritive balance.
Ooops, that wasn't a "quick word". Well, hope it helps.
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