He needs to be checked out by his doctor to determine the cause of this. It may be GERD (acid reflux) but he needs to know for sure, and there is medication for this. GERD can cause a cough and gagging during and after eating, so have him see his doctor for an evaluation and medication to relieve this. Best wishes.
have you gotten him checked out for issues with his gag reflexes. he might be having a hard time chewing his food get him checked out and if that comes he might be at time for pureed food or smaller food. what other signs is he showing for you to think he has an eating disorder issue.