Hi A.,'
Lots of good ideas here, let me throw one into the ring:
your detergent may be the cause. Years ago, I had a bad rash 'down there' and my (very bad) doc suggested I might have some contracted some nasty social disease. Sooo unlikely. Well, I switched laundry detergents and Voila!, rash and irritation gone. (this has since happened to a few friends, so it's more common than it seems).
Aside from switching detergent and running things on an extra rinse,you could check to see if there's something (stitching, fabric) in his underpants that could be lightly abrading the skin. This will also cause stinging.
And you can rinse diapers wipes out completely in a couple sinks full of water and use them this way to wipe your son. The fibrous toilet paper rubbing on the area may be exacerbating things.
Hope your son finds some relief. What a frustrating way to use the toilet!