I hope you still aren't taking any sort of weight-loss pills, powders, shakes or anything of that sort. God knows most of that stuff never gets inspected by the FDA; could be made from dehydrated bat dung for all you know. Needless to say, you probably learned your lesson about taking that stuff and letting it mess you up.
Hurting tonsils? Do you have any sort of white film on your tonsils, tongue or in the inside of your mouth? That's usually a sign of thrush, which is, as I understand it, a type of yeast infection. It has been tentatively concluded that you can get yeast infections (aka yeast overgrowth) in your intestines, and that when you have a yeast infection somewhere else, like the bladder (UTI), vagina (for women), or in the mouth (thrush), then it might be that you have too much yeast in your bowels too.
You could try and ask your GI to give you a breathalyzer to check for bacterial imbalance. You basically breathe into a tube and it analyzes the gases you expel. It knows what a normal person should be expelling, but if you breathe out too much of something, then it knows you have something in your guts producing gases it shoulnd't be producing. It's still a realitvely new test, so your GI might not have access to it (may not have even heard about it, although it's been around at least a year now).
If you can't get anywhere with that, you can try to self treat. You can take probiotics to try and get more good stuff put back in your bowels and try to force the bad stuff out. It's easier if the doctors will give you antbiotics to kill the bad stuff first, but several months on probiotics might do just as well. You can get good bacteria by eating yogurt (like Activia) or drinking acidophillus milk. But they don't have a whole lot of bacteria in them. The best thing to take is Culturelle or Digestive Advantage. They have a lot more strains of bacteria and a lot more of it, so it gives you a bigger hit at a time. The only thing is that probiotic pills like that can take some getting used to, just like fiber. In other words, they can make you gassier. If you find that you aren't tolerating them well, you can try weaning yourself onto them by starting out with a yogurt or two a day and the acidophillus milk (if you take milk), and then, after two or three weeks, try taking one probiotic pill. I take mine at night so I can sleep through the worst of the gassiness.