It confuses me why he is afraid of his litter box all of a sudden, could it be the litter makes his paws sore?
That is quite possible. You could try just the carefresh for a while to see if that helps.Be sure to check his hocks.
Is it possible something spooked him while in the litter box? Would that cause him to stop using it?
Again, quite possible and it can stop them wanting to use it. Have you moved the box from the usual spot at all? Could you make it feel like a more secure place by placing some sheets of cardboard around a couple sides?
With this going on for 2 months, I’m more inclined to think it is more to do with the feel of the litter then being scared of the spot. Definitely experiment with some softer litter or even just a puppy pee pad in the box to test the theory. That’s not a long term solution but may show if it’s something about the surface or smell he doesn’t like.
If what you do at home does not remedy the situation, I echo tobyluv’s suggestion of getting him checked out. Talk with your vet about a urine test and perhaps a blood test for E. cuniculi.