You said..."There was no specific test for bacterial or viral (should there be?)"...I think the tests would have to be done with a biopsy unless there was an exudate that could be collected from the marks....but don't forget, I'm not a vet. I know that the "pimples" on the one in the picture I posted were tested for bacteria, virus and fungus.
You said..."the first treatment was an ointment for bacterial and viral, while waiting for the fungal culture to grow. That didnt help, in fact things appeared worse. then we did the antibiotic. Trucker remained unhappy, and nothing improved. Next she wants to do a biopsy"...I would think that is the next logical step.
You said..."If there is a specific test I should ask for, feel free to let me know"....I don't know what to tell you on this....except that testing for bacteria, virus and fungus I would hope would lead to some results.
You said..."she is reading up and consulting with vets on the mainland. She is open to my suggestions and questions. So let me know please if you have a suggestion I should pass on."...she sounds like a good vet! I don't know what to suggest aside from what has already been said. The only other comment I can make is that some of the fungi will only show up with particular stains...but I can't tell you much more than that about it. Also, some fungi require more than just a topical treatment.
I hope you and the vet can figure out what's going on and bring your chameleon back to good health! Keep me posted! I'll try to post more about that type of lesion "pimples" later. It will require me doing some searching for the articles about it.)