Tina, From your original statement that the pain started behind your eye, it sounds like a sinus infection. There is one right there. It is easy for mucus filled with germs to drain out of the sinuses and down the throat. If you are lying down, or blow your nose, they can get into the eustachian tubes and into the middle ear.
I had some GERD until I was in an accident that pushed my stomach partly into my chest, requiring surgery - Nissen fundoplication. Some people have sore throats and breathing trouble from GERD. I didn't. You are doing the right thing talking to your doc about your GERD med not helping you enough. It could get better if you get the infection cured. A quart of mucus (you can produce 2 a day) surely will not make the stomach happy.
You could talk to your ENT doctor about the antibiotic not working, also about using a decongestant. Don't take antihistamines that dry out the sinuses as you want more mucus to flush out the germs (not necessarily bacteria, could be a mold or yeast or a combination). My stomach is hurting from the double dose of antibiotics I'm prescribed, and it's only 2 days of treatment. Taking antibiotics with food helps. I'm taking probiotics in between doses because I get awful gas pains when my intestinal flora gets out of whack. I hope to last out the treatment. Last time I didn't make it, and now I'm on a double dose. I'm on Septra, a sulfa drug, which is much better than most antibiotics at getting to the source of the infection.
Hang in there! It's not a one-treatment-fits-all problem. I've been fighting this for 2 years.