I just went through this myself so I totally feel for you! My baby is 6 weeks now but a few weeks ago we were experimenting with every bottle and nipple combination on the market (I was not able to breast feed and boy did this experience make the guilt and heartbreak of that even worse!!). Ultimately, we concluded it was nothing more than a phase. He would cry and grunt and squirm around like crazy while eating but his symptoms did not quite match those of reflux. He is a frequent tooter but they seem to come on out without too much fuss; same with pee, poop, and burps. I did buy the mylicon drops and at times we have thought they helped (same with gripe water) and at other times we thought they did nothing. My son actually likes the mylicon drops (not so for gripe water) so I don't hesitate to try those once a day or so but its very hit or miss. I thought it could be the flow of the formula through the nipple so tried all combinations of that and nothing seemed to make a difference. Eventually it faded and right now he is fine. He had the occasional fussy feeding but its not nearly all the time anymore. Our pediatrician said it can be just part of their little systems getting used to digestion, every sensation is brand new, etc.
One other thing we did was our dr had us drop off a poopy diaper to the office and they ran a test too see if he was lactose intolerant. For him it was negative. If you're formula-feeding you could ask your dr's office to do this as well; if it had been positive we would have had to switch to a soy-based formula. If you're nursing then I think you have to cut dairy out of your diet.
If it helps, here's what I was told to look for:
Reflux: he would arch his back, squim, grunt, fuss while eating and he would not be able to lay flat. not all babies with reflux spit up a lot; sometimes they have the pain without the spitting up, but the key symptom accoring to our dr was the inability to lay flat without crying because the acid would be creeping up in that position and causing dicomfort.
Lactose intolerance: green poop or otherwise weird poop, upset stomach between feedings, sometimes gas
Just a phase: if nothing else makes sense! For us that's what it was, as nothing else fit and the symptoms were inconsistent.
Good luck and hang in there!