litter box obsession
I don't know what you have tried so far, but the absolutely first thing I would do is take him to the vet and make sure he has no intestinal parasites or urinary elimination problems, such as infection or bladder crystals.
Next I would consider changing his litter (clumping to non-clumping or vice-versa). Add a second box next to the first and see if he has a preference. You can also experiment with texture. Some cats prefer a finer or more coarse sand. He may feel that a larger, non-clumping litter is not covering to his satisfaction. Unfortunately the litter choice is up to the cat, not us. He also may prefer a hooded or deeper box...I don't know what you currently use.
I have a cat that as a kitten would run into the box whenever another cat left to recover the poop to his own satisfaction - fortunately he has grown out of that habit!
Whatever you do, don't discourage or distract his compulsion. Like you said, at least he's using the box!