Detox reaction
Our bodies usually give us many signals before we become sick. Your acidic gut was probably so plugged up just had no where else to go but up.
It is highly likely that your body is not digesting and eliminating food properly.
While you are getting your body used to ACV, I would try an African recipe that Owen posted is CureZone for proper elimination.
Add six or seven grains of unbleached brown rice to distilled water in a one gallon glass container(Some Apple Cider Are Glass)and let it sit for a day or two. Putting it in the sun for a few hours could speed up the process. Soaking the rice in distilled water properly mineralizes the water. Start drinking six to seven glasses of distilled water with the added rice each day. When you are finished with your gallon of mineralized water, dump out the rice and distilled water and replace them. If you get three jugs, you can just rotate the gallon jugs and not have to wait. Rotate the water in your refrigerator to get the most mineralized water for daily consumption. This method will help with your highly acidic digestive system.
ACV is my favorite food for healing but it may be too much for you and too soon.
Detox reactions are rare with ACV but not unheard of. Perhaps you are so acidic that the acid is backed up into your throat? If you choose to continue ACV, go very slow. Instead of a tablespoon, you might try 1/2 of a teaspoon and increase it when your body says it is okay. Listen to your body. It is telling you that you hit the spot but go slow... Get in tune with your body.