[anonymously]

“We assumed the grain allergy. However with Cystine stones, he has a genetic defect and cannot process animal protein”.

Don’t assume anything regarding allergies. Unless the dog has been examined and tested by a board certified dermatologist. http://www.acvd.org/

The diets recommended for struvite or calcium oxalate bladder stones may not apply to your dog, the type of stones he has require a specific diet and treatment (like the one your vet recommended).

I would work closely with your veterinarian or find a veterinarian that specializes in Internal Medicine, do you have a veterinary hospital in your area? Your dog has a serious condition, this is not a DIY (imo)
http://www.caninecystinuria.com/Treatment.html http://www.dogaware.com/articles/wdjotherstones.html#cystine

PS: Have you tried the search engine at this site? Lots of information on “allergies” and “bladder stones”