just reading all of this now and I just couldnt wait to say something!! I am glad that your kitty seems healthy though!
I have had many many many cats in the past, and foster mom cats and kittens often, have a mother and babies now.. So I have seen this problem before, YAY for you for sticking through it this long, I have been the recipient of many people not sticking it out like you!
I am glad you will change the food, I wanted to say that after I read your first post, neutered males and grocery store kibble... not a good combination! A good canned all meat food is what he should have.
Also I think it is behavioral, I had a cat once that never wanted to use the litter box again after the washing machine went into spin cycle when he was in the box, lucky I was there and saw so I could connect the dots, If I had not seen it I would have never known why he refused to go in there. Something like this could have scared your kitty at some point when you were not around and now associates the litter box with this traumatic event. I would try some positive reniforcement with the litter box and maybe research online some other desensitizing training methods, I really really hope that something works for you and your kitty GOOD LUCK!!