Adding more litter boxes actually may reinforce the problem. As you say, it gives him more choices and to a cat that may be understood as where ever I choose including anywhere in the house is acceptable. You also need to use an odor removing solution on all of the unacceptable places where he has previously peed. Cat have a much higher sense of smell than we do, so even if you can't smell it, he can. I would suggest designating one litter box in one location.
Do your 3 cats generally each have their own litter box or do they share? Is this particular cat pooping in a litter box but peeing outside of it? Have you changed brands of litter? Do you clean it daily? Are all of your cats spayed or neutered? Any of these things could be affecting his litter box use.
This question may sound a bit silly but here goes.
Jessie, are you pregnant?
ANY changes that you could think of? Moving? More people in the house lately? When did this start? What happened before it started?
did the Vet check his urine for UTI?
the same thing happened with my 7 yo male and thats what it turned out to be...struvite crystals in his urine, they usually spray to tell you 'something is hurting'...
He needed to change over from dry food onto CANNED, but refused every can food I tried.
I changed his diet to a home made recipe with lots of fluids and so far (month now) it seems to have solved the problem.
the problem COULD also be related to stray males in the yard and spraying around your property, this will upset kitty into marking his own territory??