I have a dog that surfs for treats as well so I have hooded litterboxes that I strategically place so the cats can get inside them but it is too difficult for my dog.
As far as natures miracle goes, they make a oxy one that has this wonderful citrus smell and comes in an orange bottle and I absolutely love it. When my baby was a kitten we had a few accidents. He had been going back to the same two spots in my dining room without me realizing it until I caught him one day. I used this oxy natures miracle and the room just smelled fresh and new. And every time I would walk past those two spots it would smell like a breath of fresh air for weeks after I treated the spot.
It's an oxy formula meant just for cats. I will never be without it.
As a side note: sounds like your baby is miserable and I hope he gets to feeling better. Ive heard it's not good especially for a male cat to be blocked for long periods of time so If it were me I would have him checked as soon as possible.
They make mattress covers that are suppose to be leak proof so I would check into that just for future peace of mind. Wishing you the best of luck.