Try another vet. A lot of rescue places wont adopt out kittens until they are neutered, and they do this earlier than five months. You could also try to place a couple more litter trays in the places he likes to go now. He could have been spooked by something around his litter tray without you knowing.
You should also take him to the vet to check that his waterworks are ok. Sometimes what happens is they have cistitus which hurts them when they pass urine. They associate this pain with the litter tray and will refuse to use it . It could be that he is having some pain if he keeps moving to different places to do his business. You really should rule this out before you do anything else.