Maybe it's already there, something, and the acid made you aware of it? Irunno.
I always fast before taking a trip, for better and for worse. I seldom (ever? not sure) have any stomach pains during my trips, but I do meditate/focus on the sensation of hunger, which also often keeps me chained to my body. When I do try to eat something to fill it up, I either a) fly up to the skies or b) can't muster the strength to eat whatever is given to me.
Did you try smoking cannabis? This helps (generally) with stomach aches. Don't smoke it with tobacco, just weed. In a joint, preferably, so you don't have to squint with your whole intestinal system to get it in there through a bong or anything.
Take a break from it? Meditate on your stomach, try and find if whatever is bothering you lies there, dormant, on a daily basis. During the night of my ego-death (LSA), my friend cramped up in stomach aches, which were actually located in my stomach, but I was so used to it, having lived with knots of anxiety for years. Maybe it's something similar, almost psychosomatic? Do you have dark secrets/lies you keep telling others (and yourself?) that, momentarily, come across your mind during the trips? Maybe it's not even you, at all, maybe it's a friends' problems? Did you trip by yourself? What did you drink?