I'm sorry to hear that Patches isn't feeling well. Hopefully the meds that your vet prescribed will help him. I know that if he isn't running a fever or showing other signs of a URI then the vet really can't do anything for him until he starts showing these symptoms.

When you mentioned that he was shaking his head,the first thing that I thought of was earmites. This causes cats to shake their heads, scratch their ears, and a dark wax forms in their ears. I'm sure that your vet would know to test him for this if he had them.

Prayers and positive thoughts are on the way for Patches. Please keep us updated on his condition.