bowel movements are still loose

My appendix burst in April of 2009; a few days after I had surgery to remove the burst appendix and the related infections. 30cm of my small intestine and a small part of my colon had to be removed. It\'s been almost a year and a half since then and I\'m still experiencing problems. My bowel movements are still loose (and sometimes acidic if I\'ve had anything with caffeine); I\'ve been taking protein shakes which actually help substantially, but if I stop for more than a couple days they go back to being loose again. I also get a pain in my upper stomach if I run for more than a couple miles, and I feel like I\'m going to puke. Last but not least, my ability to drink alcohol is all but gone; I can\'t take more than a few shots or beers without getting that pain in my upper stomach again and puking. Is something else wrong with me? Is it just a slow healing process, or will I always be like this?