I'm guessing you've had him to the vet to make sure there's no lingering physical ailments, right?
He may be associating the box with at least some discomfort from when he was sick. I'd probably get two boxes (I know, I don't have room for enough boxes in my place either, but two is definitely good, in different locations), and try Cat Attract (or maybe Kitten Attract since he's so young). Maybe even get brand new boxes, just in case there's somehow an off odor in the existing box. And, check with a black light to make sure you've gotten all the odors up. Zero Odor is good too, but it's mail order only right now. OK, I'm also assuming you're scooping twice a day or so -if not, you may want to increase your frequency.
You can't really discipline him, since he won't know why you're disciplining him. If you catch him literally in the act, gently pick him up and put him in the box, but never yell at him or make him feel that the act of going itself is somehow bad.
I had very good luck with Cat Attract, and I've got a boy who's just picky about his boxes.