Avocado, I hope you don't mind one more question.
I already asked about the drinking water, now something else.
Have you ever observed how far Francis opens his mouth when he yawns?
If not, please do that.
Whether he opens his mouth wide, all the way, or not, is very important and can help you come closer to determining what the problem is. Because, no matter how we look at it, a cat should not be uncomfortable chewing his food. Always uncomfortable as you put it.
Since cats (like people) can suffer from TMJ syndrome for example, I can't help wondering if maybe that's what's wrong with your kitty. If your vet is not thinking of this possibility, the problem can go undiagnosed and consequently untreated.
I still believe you should have your kitty seen by a veterinary dentist.