I agree with Kandy. I can tell you how frustrating it is to have the doctor dismiss side effects as something unrelated, only to find out later that they disappear when the meds are changed...usually after months of suffering. If there is any chance that it might be a reaction to the stilbesterol, changing her over to phenylpropanolamine would be an easy enough thing to do.
I don't know enough about the possible side effects, however, to know how many of the other symptoms the vet found could be caused by the hormone replacement.