I had some pretty bad GI issues in the last days of my drinking as well. I didn't even really eat much, I drank many of my meals. I had horrible heartburn that kept me up ( when I wasn't passed out drunk ) and bad reflux to the point of spasms out of the blue sometimes. Other bad issues with things at the other end of GI tract too not worth repeating here.
Almost all of those issues got better after I was sober for a while and started eating better. You need to give it time though - it's not going to improve in just a matter of days after quitting unfortunately.