Pain During Nail Clipping

Try filing them. I used to have to literally sit on top of my eldest daughter; she insisted that it hurt (she was just terrified of the clippers)... I switched to a file which helped for a while, then she finally started doing it herself! I have super sensitive nails... the connective tissue under my nails comes up really high and so my nails ALWAYS have to be long to a certain extent or it 'feels weird' like your son says. Try teaching him to file his nails himself (supervised), then graduate to those clippers!

This might be coming from left feild but many Austitic kids are very sensitive to getting their hair and nails cut. Does he show any signs of Austisim?

Have you tried doing it in or after the bath? My own nails practically snap when I clip them, but I do my kids in the bath, because they get really soft and they sort of tear away pretty smoothly.

I used to hate my mom clipping my nails too, I still remember it. I would fight her. It didnt hurt to have them clipped but I hated the way they felt afterwards, the sensitivity of the tips now being more exposed, I hated to touch stuff, seems like it would take a day or two for that weird feeling to go away.
Then, I turned into a nail biter because I didnt want her clipping them, and I still struggle with that if I dont have acrylics.
Maybe teaching him to file them himself would be a good alternative, or maybe you just filing them and do it a little more often than necessary so they dont get too long and leave that sensitive feeling afterwards.

Try nail scissors instead of clippers. The scissors don't give that small shock feeling like clippers and they give you more control. I find that it's almost impossible to cut too close using nail scissors. After a bath and with scissors, nails can be cut without much sensation at all.