I was told that the cells of our lymph nodes have a certain look under the microscope. They do not look like squamous cell carcinoma cells. When they look under the microscope they can easily tell the difference.
There is a very small margin of error for this with fine-needle biopsy, but it seems in your case this check was done after they removed the lymph node - the margin of error in this case is - practically - negligible.
The PET scan will find any abnormal lymph node that is larger than 5mm. (Based upon the fact that abnormal lymph nodes take up substantially more sugar.) Based on this, they can vary the drug choice of the chemotherapy and the radiation target.
I had a very similar ordeal a year ago (large lymph node on one side), in my case they could not find the primary tumor - this happens about 5-10% of the cases. I got chemo with cisplatin and general radiation to the affected side of my neck.
Good luck to you! The treatments are very rough, but we do recover once they are done.