Since the gallbladder is only a pouch hanging off the common bile duct it collects stones and sludge that come down from the small bile ducts in the liver. You most likely have more stones still up in these ducts, parasites and even bacteria growing these. It is important to do the preparations - parasite cleanse and a method of dissolving or softening hard calcium stones so that these can be flushed out. See Clark''s Kidney Cleanse, Moritz's apple juice/malic acid, gold coin grass.
Since you have low vitamins you may have a maladsorbtion syndrome. There are many causes of this but a person needs to rule out the various problems related to gluten sensitivity or intolerance, especially Celiac Disease.