When I stopped drinking back in December I noticed my throat was sore quite a bit, especially late in the evening. Great, I thought, I stop drinking and smoking and things get worse, not better, grrrr!
I went to the doctor in Jan and their thought was acid reflux. They've given me a course of meds to calm down my stomach. They seems to be working.
Whether or not this is related to alcohol is unknown (the doctor didn't say one way or the other), but I think one of the things I've realised is that life goes on. There would have been illnesses/stomach problems/health issues regardless of whether the drinking continued or not. But as other posters have said, eliminating alcohol is only going to improve the probability of not getting ill, and vastly improve the probability that the health issue won't be the direct result of the alcohol!