Some of your symptoms could be indications of Crohn's Disease. Another consideration, although unlikely, is malabsorption with mineral deficiencies as the cause of the muscle pains. Food allergies may be contributing to your symptoms but it is difficult to prove this diagnosis. You do not provide your age or other medical history, information that could direct workup in this direction. Your letter does illustrate an important feature of reflux disease.
Acid reflux is a chronic problem.
Symptoms may be present for years, although the severity can fluctuate. Medical treatment can be lifetime. Surgery can improve symptoms and eliminate the need for medication. If surgery is considered, an esophageal motility study should be done pre-operatively to exclude any esophageal motility problems that could cause problems in the postoperative period. This response is offered for your general information and should not replace the conclusions drawn from a careful and complete evaluation by your physician.