I agree with Ladyjane. Prescription diets are necessary in some cases. My sister's little Jack Russell had the same issues your Yorkie did. From the time she was six months old she kept developing crystals - no infection, no stones, just crystals. Her vet was stumped so she referred her to NC State Vet School and they ran extensive tests with no conclusive findings. She was put on Waltham prescription kidney diet for life.
If you are really opposed to prescription food, I would suggest consulting a certified canine nutritionist and homecooking. We have a list pinned in the YT library.
http://www.yorkietalk.com/forums/yor...itionists.html
I would absolutely stop feeding raw. It is not appropriate for dogs with health issues.