as the omnipresent effects of alcohol are lifted, underlying conditions start to show up. also, as you noted, as our bodies start to heal, they tend to expel a lot of crap, one way or another!! you are in early days, treat yourself gently, acknowledge the symptoms, treat them accordingly.
in real life, allergies happen. colds happen. headaches happen. none require alcohol.
it has been said that often low grade headaches can actually be a sign of being dehydrated. can't say enough good stuff about good ole WATER.