I'm guessing it could partially be the theobromine, which acts as a vasodilator.

It might open up the blood vessels and cause swelling and irritation - the
opposite effect that caffeine has - which is a vasoconstrictor and reduces the
swelling in the brain so it's not grinding up against the inside of your skull
when you have a throbbing headache.

Chocolate is also known to contain oxalic acid, which I'm guessing is the main
culprit.  It will instantly combine with calcium in your blood to form
needle-shaped calcium oxalate crystals which produce an intense burning
sensation in the mouth.

Get some Anbesol, or see if some tea or coffee (tannins) will form a protective
coating over the affected area.

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