Unfortunately, I dont have any advice/ideas on your problems but I did want to say CONGRATS on your sobriety and I hope you stick with it!!! :-)
First, congratulations on your sobriety. Keep it up! (The pastor at my church went through the same thing as you, and he describes a lot of it in detail: calvaryftl.org.)
Second, your symptoms could be a LOT of things, including your body adjusting to your sobriety. Particularly, the bacteria in your stomach could be adjusting their levels. So before anything else, I recommend getting on probiotics. You can pick these up at any health food store.
Of course, considering what you've put your body through, again it could be a lot of other things, so you might want to consider visiting a gastroenterologist about your symptoms, just to make sure it's nothing serious. (Your entire gastrointestinal system has taken a pretty big hit.) However, I would first and foremost recommend the probiotics. (The "Activia" yogurt, I've found, is very helpful, so if you can't find a health store near you, look for that at any grocery store, instead.)
Good luck, and again, congratulations.