Hi Prashanth, i'm also going through the exact same thing, i have recently fount out i have gerd, wich is acid that is flowing up to your throat you might wan to get that checked out ;)
By the way, if you haven't gone through an elimination diet to figure out your own food sensitivity issues yet, this will greatly help improve your overall symptoms. A naturopath can help you go through this process, so you'll know what your personal food triggers are. There is a list of the most common food sensitivities, which are like hidden food allergies, that the naturopath will give you to avoid for a minimum of two weeks before you start the process of elimination to learn what your food sensitivities are. It takes a long time to go through an elimination diet, but it's worth the temporary frustration because avoiding your food triggers will improve your IBS/GERD symptoms, which should include having better breath. One of the most common food triggers is gluten, wheat gluten in particular.
It sounds like you have the kind of IBS that fluctuates between constipation and diarrhea. Am I right? Anyway, I have been using some natural therapies in combination with conventional therapies that are most helpful with constipation. This has been really helpful for me, since I also have GERD.
I have been taking chlorella everyday. It's a type of algae and is full of nutrients. It contains chlorophyl, too, which is known to help with stomach related bad breath. It helps with the constipation, too. My naturopath has me using Oregon grape, which is supposed to be taken with each meal. It works for me for a stool softener, since I can't use the medication in Dulcolax or Colace (same medication). I am also using cascara sagrada as the laxative. I do have to be mindful not to take too much magnesium for my body, but I was told to take between 400 and 800 mg per day. If I take it at the same time as cascara sagrada and forget to later take the calcium, then it's too much and I'll have a bout of diarrhea. So, this takes some fine tuning to the individual's needs. I don't usually get diarrhea myself.
There is a natural breath spray made of essential oils called Breath Tonic made by the company called Herb Pharm. Since it's made with essential oils, peppermint being the first one on the list, the liquid is a natural green color. Clearly, this would have a bit of chlorophyl in it, too. I have seen it available at the discount vitamin store for about $2.00 cheaper than it costs for the same thing at the local co-op. It's very potent and I have noticed that it takes care of that "something died in there" taste that I notice on myself that makes me self-conscious myself.
Also, if you're a coffee drinker, remember that coffee is a diuretic and will likely aggravate your constipation. If not drinked regularly, it may even initially trigger a bit of diarrhea, which has been my own experience. If you have GERD, you may notice that coffee will make you have bad breath, too.
I hope some of these suggestions will help. I know that taking care of the digestive issues should help with the bad breath.