Did your vet mention seborhhea? A woman once told me her previous Yorkie had that and had dark spots on tummy, very stinky, and hair loss. Here is a link to more info about it:
http://www.provet.co.uk/health/disea...alalopecia.htm
and other Yorkie Talk info that might be related:
http://www.yorkietalk.com/forums/yor...-problems.html
Also, I've heard that if you use medicated shampoo, be sure to leave it on 10 minutes before rinsing or it does no good.
Bless you for taking her in, and Good Luck!