My cousin's son had reflux for a long time and had to take medicine to control the acid (basically the equivalent to baby-nexium). He also slept more in his car seat than his bed. If your son's reflux has gone untreated for this long, he probably has damage to his esophagus, which is very painful and is probably making his reflux worse. Try elevating one side of his crib at night. If he can stay semi-upright, gravity will keep the acid down and give his throat a chance to heal.

Oh, and shoot your doctor.