This sounds like what I'm experiencing now and I'm pretty sure it's a delayed reaction to the localized anaesthesia. For me, they used lidocaine. I found one article online where they said delayed reactions are more common than first thought.
I've never had an FNA, so I can't really if this is normal or not, but I've never really heard any of our members mention hives like that, or earache; though I could just have missed it.
I have heard of pain, along the neck and jaw.
I'm sure than someone who has had FNA will be able to answer your questions more fully.
It's great that the one nodule was benign and chances are, the others will be, too, but you really should have that repeat biopsy to be sure.