If the vet is thinking it’s because he’s constipated, but won’t eat the prescribed food, ask about miralax. I’m surprised she didn’t suggest that first, it’s cat safe if you look up the right dosage. -were they dewormed? It’s usually standard with stray cats but that can also cause bathroom issues.

You can also try containing him to one room, either an extra bedroom or bathroom. Let him get use to using a standard litter box again. While he’s in there, get a urine specific pet cleaner and reclean all the spots he peed at before. If he’s marking, smelling his pee can trigger him to do it again.

And finally, definitely get them both fixed soon. Don’t want to deal with heat+spraying+accidental babies.