I literaly went to the doctor today for a alternating throat pain. They did a strep swab and a when it came out negative they pricked my finger to run a quick blood test. It's been going on for a week now, my throat will hurt then it won't, then it will be painful, then the pain will move to a different spot. It was so bad last night I could't talk and was almost in tears. Anyway the doctor said I had a bacterial infection and prescribed me Azithromycin (antibiotic) and prednisone (steroid) for the pain. It sounds similar except for the eyes. If it is bacterial it can be serious because it can get into your blood stream and turn into something even worse. (So says my doctor.) I'd get it checked out just to make sure.
It's probably an infection, painful glands are one of the symptoms. It could be viral or bacterial. I've had pain alternating from one side to the other too.