Confine the kitten to one room with the 2 trays, food and water so it learns where the trays will be
Also ensure the litter trays are away from heavy household traffic he may be being spooked by something when going for Number 2's and is associating bad things with the tray
I know its a pain but try mixing some compost with litter he may not like whats under his paws, here we use wood pellet, clumping clay - fine and normal sizes, paper and one good old compost for Riley feral