Have you checked for infection; ear mites, etc?
Yes - his ears are clean. It's not that they hurt from infection. He's not bad about flipping the ear back and looking inside, it's if you grab or hold his ear flap itself that he cries and pulls away.
As a flop-eared-dog touchy about his ears, I sortof dread ear infections in him, my old lab got them a lot, and Homer will not be good about it if he needs treated.