Does he have any other health issues? Any history of stroke or esophageal stricture? Do his eyes water or shoes his nose run when he eats? Could be aspiration. You can always start at your primary care physician.
Excerpt from the article "8 Most Common Food Intolerances You May Not Know You Have"..
"Signs that you may be suffering a food intolerance include:
Migraines or headaches
Skin rashes or hives
A stuffy or runny nose
A general feeling of unwellness without an apparent cause"