Acidity, indigestion, gall stones,

I have constant indigestion problem. I never get clear motions and have to use the toilet at least 3 times a day. I have problem in digesting milk, eggs, protein. 2 weeks back I had severe pain in lower abdomen. I had consumed mashroom and corn. The pain has gone after course of antibiotics. but still indigestion issues are there. motions are not clear. I am also having 3 gall bladder stones, largest with 8 mm thickness. I also have problem whenever I consume chili. My stomach gets bloated very often. I also face pain in upper abdomen during evenings. I am taking calcium and iron daily for the past 3 months. However I had these stomach problems even before taking these supplements also. I am also taking thyronorm 50mcg for the past 10 years. Pls suggest.